Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 7 transcript(s)...
Querying Taster for transcript #1: ENST00000373190
Querying Taster for transcript #2: ENST00000373187
Querying Taster for transcript #3: ENST00000373193
Querying Taster for transcript #4: ENST00000356100
Querying Taster for transcript #5: ENST00000373198
Querying Taster for transcript #6: ENST00000373184
Querying Taster for transcript #7: ENST00000373201
MT speed 0 s - this script 5.087871 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
PTPRTpolymorphism_automatic0.112584108240279simple_aaeaffectedA29Psingle base exchangers2867655show file
PTPRTpolymorphism_automatic0.112584108240279simple_aaeaffectedA29Psingle base exchangers2867655show file
PTPRTpolymorphism_automatic0.112584108240279simple_aaeaffectedA29Psingle base exchangers2867655show file
PTPRTpolymorphism_automatic0.112584108240279simple_aaeaffectedA29Psingle base exchangers2867655show file
PTPRTpolymorphism_automatic0.112584108240279simple_aaeaffectedA29Psingle base exchangers2867655show file
PTPRTpolymorphism_automatic0.112584108240279simple_aaeaffectedA29Psingle base exchangers2867655show file
PTPRTpolymorphism_automatic0.112584108240279simple_aaeaffectedA29Psingle base exchangers2867655show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.887415891759721 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:41818289C>GN/A show variant in all transcripts   IGV
HGNC symbol PTPRT
Ensembl transcript ID ENST00000373190
Genbank transcript ID N/A
UniProt peptide O14522
alteration type single base exchange
alteration region CDS
DNA changes c.85G>C
cDNA.194G>C
g.322G>C
AA changes A29P Score: 27 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 29
frameshift no
known variant Reference ID: rs2867655
databasehomozygous (G/G)heterozygousallele carriers
1000G14287052133
ExAC583107690
regulatory features H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
Non-Gene Associated, Regulatory Feature, Non-Gene associated regulatory feature
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)1.8861
1.8861
(flanking)0.1471
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost325sequence motif lost- wt: GCAG|gtga
 mu: CCAG.gtga
Donor marginally increased324wt: 0.9951 / mu: 0.9960 (marginal change - not scored)wt: GCCGCAGGTGAGTGC
mu: GCCCCAGGTGAGTGC		 CGCA|ggtg
Donor gained3200.47mu: GAGCGCCCCAGGTGA GCGC|ccca
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      29PPLPGARAQSAAGGCSFDEHYSNC
mutated  not conserved    29PPLPGARAQSAPGGCSFDEHYSN
Ptroglodytes  all identical  ENSPTRG00000013505  29PPLPGARAQSAAGGCSFDEHYSN
Mmulatta  no alignment  ENSMMUG00000001108  n/a
Fcatus  no alignment  ENSFCAG00000004770  n/a
Mmusculus  all identical  ENSMUSG00000053141  29PPLPGAGAQSAAGGCSFDEHYSN
Ggallus  no alignment  ENSGALG00000003488  n/a
Trubripes  no alignment  ENSTRUG00000008419  n/a
Drerio  no alignment  ENSDARG00000074781  n/a
Dmelanogaster  no alignment  FBgn0014007  n/a
Celegans  no alignment  F56D1.4  n/a
Xtropicalis  no alignment  ENSXETG00000012126  n/a
protein features
start (aa)end (aa)featuredetails 
26747TOPO_DOMExtracellular (Potential).lost
30191DOMAINMAM.might get lost (downstream of altered splice site)
6060CONFLICTW -> T (in Ref. 1; AAD09421).might get lost (downstream of altered splice site)
7878CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
9898CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
137137CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
193284DOMAINIg-like C2-type.might get lost (downstream of altered splice site)
208208CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
213213DISULFIDBy similarity.might get lost (downstream of altered splice site)
267267DISULFIDBy similarity.might get lost (downstream of altered splice site)
288379DOMAINFibronectin type-III 1.might get lost (downstream of altered splice site)
375375CONFLICTP -> A (in Ref. 1; AAD09421).might get lost (downstream of altered splice site)
386480DOMAINFibronectin type-III 2.might get lost (downstream of altered splice site)
421421CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
481584DOMAINFibronectin type-III 3.might get lost (downstream of altered splice site)
510510CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
547547CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
589726DOMAINFibronectin type-III 4.might get lost (downstream of altered splice site)
601601CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
654654CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
684684CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
748768TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
7691441TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
867867CONFLICTP -> L (in Ref. 1; AAD09421).might get lost (downstream of altered splice site)
871873HELIXmight get lost (downstream of altered splice site)
874882HELIXmight get lost (downstream of altered splice site)
889895HELIXmight get lost (downstream of altered splice site)
8891143DOMAINTyrosine-protein phosphatase 1.might get lost (downstream of altered splice site)
905908TURNmight get lost (downstream of altered splice site)
910915HELIXmight get lost (downstream of altered splice site)
925927HELIXmight get lost (downstream of altered splice site)
938941HELIXmight get lost (downstream of altered splice site)
944948STRANDmight get lost (downstream of altered splice site)
951953STRANDmight get lost (downstream of altered splice site)
957960STRANDmight get lost (downstream of altered splice site)
965967TURNmight get lost (downstream of altered splice site)
968978HELIXmight get lost (downstream of altered splice site)
982985STRANDmight get lost (downstream of altered splice site)
989991STRANDmight get lost (downstream of altered splice site)
10031009STRANDmight get lost (downstream of altered splice site)
10111020STRANDmight get lost (downstream of altered splice site)
10221033STRANDmight get lost (downstream of altered splice site)
10401047STRANDmight get lost (downstream of altered splice site)
10521052BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
10601072HELIXmight get lost (downstream of altered splice site)
10801083STRANDmight get lost (downstream of altered splice site)
10841084ACT_SITEPhosphocysteine intermediate (By similarity).might get lost (downstream of altered splice site)
10841090REGIONSubstrate binding (By similarity).might get lost (downstream of altered splice site)
10851088STRANDmight get lost (downstream of altered splice site)
10891107HELIXmight get lost (downstream of altered splice site)
11081110STRANDmight get lost (downstream of altered splice site)
11121122HELIXmight get lost (downstream of altered splice site)
11281128BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
11301145HELIXmight get lost (downstream of altered splice site)
11751437DOMAINTyrosine-protein phosphatase 2.might get lost (downstream of altered splice site)
13781378ACT_SITEPhosphocysteine intermediate (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 4323 / 4323
position (AA) of stopcodon in wt / mu AA sequence 1441 / 1441
position of stopcodon in wt / mu cDNA 4432 / 4432
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 110 / 110
chromosome 20
strand -1
last intron/exon boundary 4379
theoretical NMD boundary in CDS 4219
length of CDS 4323
coding sequence (CDS) position 85
cDNA position
(for ins/del: last normal base / first normal base)		 194
gDNA position
(for ins/del: last normal base / first normal base)		 322
chromosomal position
(for ins/del: last normal base / first normal base)		 41818289
original gDNA sequence snippet GCGCCCGGGCTCAGAGCGCCGCAGGTGAGTGCGCCCGCCCG
altered gDNA sequence snippet GCGCCCGGGCTCAGAGCGCCCCAGGTGAGTGCGCCCGCCCG
original cDNA sequence snippet GCGCCCGGGCTCAGAGCGCCGCAGGTGGCTGTTCCTTTGAT
altered cDNA sequence snippet GCGCCCGGGCTCAGAGCGCCCCAGGTGGCTGTTCCTTTGAT
wildtype AA sequence MASLAALALS LLLRLQLPPL PGARAQSAAG GCSFDEHYSN CGYSVALGTN GFTWEQINTW
EKPMLDQAVP TGSFMMVNSS GRASGQKAHL LLPTLKENDT HCIDFHYYFS SRDRSSPGAL
NVYVKVNGGP QGNPVWNVSG VVTEGWVKAE LAISTFWPHF YQVIFESVSL KGHPGYIAVD
EVRVLAHPCR KAPHFLRLQN VEVNVGQNAT FQCIAGGKWS QHDKLWLQQW NGRDTALMVT
RVVNHRRFSA TVSVADTAQR SVSKYRCVIR SDGGSGVSNY AELIVKEPPT PIAPPELLAV
GATYLWIKPN ANSIIGDGPI ILKEVEYRTT TGTWAETHIV DSPNYKLWHL DPDVEYEIRV
LLTRPGEGGT GPPGPPLTTR TKCADPVHGP QNVEIVDIRA RQLTLQWEPF GYAVTRCHSY
NLTVQYQYVF NQQQYEAEEV IQTSSHYTLR GLRPFMTIRL RLLLSNPEGR MESEELVVQT
EEDVPGAVPL ESIQGGPFEE KIYIQWKPPN ETNGVITLYE INYKAVGSLD PSADLSSQRG
KVFKLRNETH HLFVGLYPGT TYSFTIKAST AKGFGPPVTT RIATKISAPS MPEYDTDTPL
NETDTTITVM LKPAQSRGAP VSVYQLVVKE ERLQKSRRAA DIIECFSVPV SYRNASSLDS
LHYFAAELKP ANLPVTQPFT VGDNKTYNGY WNPPLSPLKS YSIYFQALSK ANGETKINCV
RLATKGASTQ NSNTVEPEKQ VDNTVKMAGV IAGLLMFIII LLGVMLTIKR RRNAYSYSYY
LKLAKKQKET QSGAQREMGP VASADKPTTK LSASRNDEGF SSSSQDVNGF NGSRGELSQP
TLTIQTHPYR TCDPVEMSYP RDQFQPAIRV ADLLQHITQM KRGQGYGFKE EYEALPEGQT
ASWDTAKEDE NRNKNRYGNI ISYDHSRVRL LVLDGDPHSD YINANYIDGY HRPRHYIATQ
GPMQETVKDF WRMIWQENSA SIVMVTNLVE VGRVKCVRYW PDDTEVYGDI KVTLIETEPL
AEYVIRTFTV QKKGYHEIRE LRLFHFTSWP DHGVPCYATG LLGFVRQVKF LNPPEAGPIV
VHCSAGAGRT GCFIAIDTML DMAENEGVVD IFNCVRELRA QRVNLVQTEE QYVFVHDAIL
EACLCGNTAI PVCEFRSLYY NISRLDPQTN SSQIKDEFQT LNIVTPRVRP EDCSIGLLPR
NHDKNRSMDV LPLDRCLPFL ISVDGESSNY INAALMDSHK QPAAFVVTQH PLPNTVADFW
RLVFDYNCSS VVMLNEMDTA QFCMQYWPEK TSGCYGPIQV EFVSADIDED IIHRIFRICN
MARPQDGYRI VQHLQYIGWP AYRDTPPSKR SLLKVVRRLE KWQEQYDGRE GRTVVHCLNG
GGRSGTFCAI CSVCEMIQQQ NIIDVFHIVK TLRNNKSNMV ETLEQYKFVY EVALEYLSSF
*
mutated AA sequence MASLAALALS LLLRLQLPPL PGARAQSAPG GCSFDEHYSN CGYSVALGTN GFTWEQINTW
EKPMLDQAVP TGSFMMVNSS GRASGQKAHL LLPTLKENDT HCIDFHYYFS SRDRSSPGAL
NVYVKVNGGP QGNPVWNVSG VVTEGWVKAE LAISTFWPHF YQVIFESVSL KGHPGYIAVD
EVRVLAHPCR KAPHFLRLQN VEVNVGQNAT FQCIAGGKWS QHDKLWLQQW NGRDTALMVT
RVVNHRRFSA TVSVADTAQR SVSKYRCVIR SDGGSGVSNY AELIVKEPPT PIAPPELLAV
GATYLWIKPN ANSIIGDGPI ILKEVEYRTT TGTWAETHIV DSPNYKLWHL DPDVEYEIRV
LLTRPGEGGT GPPGPPLTTR TKCADPVHGP QNVEIVDIRA RQLTLQWEPF GYAVTRCHSY
NLTVQYQYVF NQQQYEAEEV IQTSSHYTLR GLRPFMTIRL RLLLSNPEGR MESEELVVQT
EEDVPGAVPL ESIQGGPFEE KIYIQWKPPN ETNGVITLYE INYKAVGSLD PSADLSSQRG
KVFKLRNETH HLFVGLYPGT TYSFTIKAST AKGFGPPVTT RIATKISAPS MPEYDTDTPL
NETDTTITVM LKPAQSRGAP VSVYQLVVKE ERLQKSRRAA DIIECFSVPV SYRNASSLDS
LHYFAAELKP ANLPVTQPFT VGDNKTYNGY WNPPLSPLKS YSIYFQALSK ANGETKINCV
RLATKGASTQ NSNTVEPEKQ VDNTVKMAGV IAGLLMFIII LLGVMLTIKR RRNAYSYSYY
LKLAKKQKET QSGAQREMGP VASADKPTTK LSASRNDEGF SSSSQDVNGF NGSRGELSQP
TLTIQTHPYR TCDPVEMSYP RDQFQPAIRV ADLLQHITQM KRGQGYGFKE EYEALPEGQT
ASWDTAKEDE NRNKNRYGNI ISYDHSRVRL LVLDGDPHSD YINANYIDGY HRPRHYIATQ
GPMQETVKDF WRMIWQENSA SIVMVTNLVE VGRVKCVRYW PDDTEVYGDI KVTLIETEPL
AEYVIRTFTV QKKGYHEIRE LRLFHFTSWP DHGVPCYATG LLGFVRQVKF LNPPEAGPIV
VHCSAGAGRT GCFIAIDTML DMAENEGVVD IFNCVRELRA QRVNLVQTEE QYVFVHDAIL
EACLCGNTAI PVCEFRSLYY NISRLDPQTN SSQIKDEFQT LNIVTPRVRP EDCSIGLLPR
NHDKNRSMDV LPLDRCLPFL ISVDGESSNY INAALMDSHK QPAAFVVTQH PLPNTVADFW
RLVFDYNCSS VVMLNEMDTA QFCMQYWPEK TSGCYGPIQV EFVSADIDED IIHRIFRICN
MARPQDGYRI VQHLQYIGWP AYRDTPPSKR SLLKVVRRLE KWQEQYDGRE GRTVVHCLNG
GGRSGTFCAI CSVCEMIQQQ NIIDVFHIVK TLRNNKSNMV ETLEQYKFVY EVALEYLSSF
*
speed 0.48 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.887415891759721 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:41818289C>GN/A show variant in all transcripts   IGV
HGNC symbol PTPRT
Ensembl transcript ID ENST00000373187
Genbank transcript ID NM_007050
UniProt peptide O14522
alteration type single base exchange
alteration region CDS
DNA changes c.85G>C
cDNA.85G>C
g.322G>C
AA changes A29P Score: 27 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 29
frameshift no
known variant Reference ID: rs2867655
databasehomozygous (G/G)heterozygousallele carriers
1000G14287052133
ExAC583107690
regulatory features H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
Non-Gene Associated, Regulatory Feature, Non-Gene associated regulatory feature
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)1.8861
1.8861
(flanking)0.1471
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost325sequence motif lost- wt: GCAG|gtga
 mu: CCAG.gtga
Donor marginally increased324wt: 0.9951 / mu: 0.9960 (marginal change - not scored)wt: GCCGCAGGTGAGTGC
mu: GCCCCAGGTGAGTGC		 CGCA|ggtg
Donor gained3200.47mu: GAGCGCCCCAGGTGA GCGC|ccca
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      29PPLPGARAQSAAGGCSFDEHYSNC
mutated  not conserved    29PPLPGARAQSAPGGCSFDEHYSN
Ptroglodytes  all identical  ENSPTRG00000013505  29PPLPGARAQSAAGGCSFDEHYSN
Mmulatta  no alignment  ENSMMUG00000001108  n/a
Fcatus  no alignment  ENSFCAG00000004770  n/a
Mmusculus  all identical  ENSMUSG00000053141  29PPLPGAGAQSAAGGCSFDEHYSN
Ggallus  no alignment  ENSGALG00000003488  n/a
Trubripes  no alignment  ENSTRUG00000008419  n/a
Drerio  no alignment  ENSDARG00000074781  n/a
Dmelanogaster  no alignment  FBgn0014007  n/a
Celegans  no alignment  F56D1.4  n/a
Xtropicalis  no alignment  ENSXETG00000012126  n/a
protein features
start (aa)end (aa)featuredetails 
26747TOPO_DOMExtracellular (Potential).lost
30191DOMAINMAM.might get lost (downstream of altered splice site)
6060CONFLICTW -> T (in Ref. 1; AAD09421).might get lost (downstream of altered splice site)
7878CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
9898CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
137137CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
193284DOMAINIg-like C2-type.might get lost (downstream of altered splice site)
208208CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
213213DISULFIDBy similarity.might get lost (downstream of altered splice site)
267267DISULFIDBy similarity.might get lost (downstream of altered splice site)
288379DOMAINFibronectin type-III 1.might get lost (downstream of altered splice site)
375375CONFLICTP -> A (in Ref. 1; AAD09421).might get lost (downstream of altered splice site)
386480DOMAINFibronectin type-III 2.might get lost (downstream of altered splice site)
421421CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
481584DOMAINFibronectin type-III 3.might get lost (downstream of altered splice site)
510510CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
547547CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
589726DOMAINFibronectin type-III 4.might get lost (downstream of altered splice site)
601601CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
654654CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
684684CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
748768TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
7691441TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
867867CONFLICTP -> L (in Ref. 1; AAD09421).might get lost (downstream of altered splice site)
871873HELIXmight get lost (downstream of altered splice site)
874882HELIXmight get lost (downstream of altered splice site)
889895HELIXmight get lost (downstream of altered splice site)
8891143DOMAINTyrosine-protein phosphatase 1.might get lost (downstream of altered splice site)
905908TURNmight get lost (downstream of altered splice site)
910915HELIXmight get lost (downstream of altered splice site)
925927HELIXmight get lost (downstream of altered splice site)
938941HELIXmight get lost (downstream of altered splice site)
944948STRANDmight get lost (downstream of altered splice site)
951953STRANDmight get lost (downstream of altered splice site)
957960STRANDmight get lost (downstream of altered splice site)
965967TURNmight get lost (downstream of altered splice site)
968978HELIXmight get lost (downstream of altered splice site)
982985STRANDmight get lost (downstream of altered splice site)
989991STRANDmight get lost (downstream of altered splice site)
10031009STRANDmight get lost (downstream of altered splice site)
10111020STRANDmight get lost (downstream of altered splice site)
10221033STRANDmight get lost (downstream of altered splice site)
10401047STRANDmight get lost (downstream of altered splice site)
10521052BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
10601072HELIXmight get lost (downstream of altered splice site)
10801083STRANDmight get lost (downstream of altered splice site)
10841084ACT_SITEPhosphocysteine intermediate (By similarity).might get lost (downstream of altered splice site)
10841090REGIONSubstrate binding (By similarity).might get lost (downstream of altered splice site)
10851088STRANDmight get lost (downstream of altered splice site)
10891107HELIXmight get lost (downstream of altered splice site)
11081110STRANDmight get lost (downstream of altered splice site)
11121122HELIXmight get lost (downstream of altered splice site)
11281128BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
11301145HELIXmight get lost (downstream of altered splice site)
11751437DOMAINTyrosine-protein phosphatase 2.might get lost (downstream of altered splice site)
13781378ACT_SITEPhosphocysteine intermediate (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 4326 / 4326
position (AA) of stopcodon in wt / mu AA sequence 1442 / 1442
position of stopcodon in wt / mu cDNA 4326 / 4326
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 1 / 1
chromosome 20
strand -1
last intron/exon boundary 4273
theoretical NMD boundary in CDS 4222
length of CDS 4326
coding sequence (CDS) position 85
cDNA position
(for ins/del: last normal base / first normal base)		 85
gDNA position
(for ins/del: last normal base / first normal base)		 322
chromosomal position
(for ins/del: last normal base / first normal base)		 41818289
original gDNA sequence snippet GCGCCCGGGCTCAGAGCGCCGCAGGTGAGTGCGCCCGCCCG
altered gDNA sequence snippet GCGCCCGGGCTCAGAGCGCCCCAGGTGAGTGCGCCCGCCCG
original cDNA sequence snippet GCGCCCGGGCTCAGAGCGCCGCAGGTGGCTGTTCCTTTGAT
altered cDNA sequence snippet GCGCCCGGGCTCAGAGCGCCCCAGGTGGCTGTTCCTTTGAT
wildtype AA sequence MASLAALALS LLLRLQLPPL PGARAQSAAG GCSFDEHYSN CGYSVALGTN GFTWEQINTW
EKPMLDQAVP TGSFMMVNSS GRASGQKAHL LLPTLKENDT HCIDFHYYFS SRDRSSPGAL
NVYVKVNGGP QGNPVWNVSG VVTEGWVKAE LAISTFWPHF YQVIFESVSL KGHPGYIAVD
EVRVLAHPCR KAPHFLRLQN VEVNVGQNAT FQCIAGGKWS QHDKLWLQQW NGRDTALMVT
RVVNHRRFSA TVSVADTAQR SVSKYRCVIR SDGGSGVSNY AELIVKEPPT PIAPPELLAV
GATYLWIKPN ANSIIGDGPI ILKEVEYRTT TGTWAETHIV DSPNYKLWHL DPDVEYEIRV
LLTRPGEGGT GPPGPPLTTR TKCADPVHGP QNVEIVDIRA RQLTLQWEPF GYAVTRCHSY
NLTVQYQYVF NQQQYEAEEV IQTSSHYTLR GLRPFMTIRL RLLLSNPEGR MESEELVVQT
EEDVPGAVPL ESIQGGPFEE KIYIQWKPPN ETNGVITLYE INYKAVGSLD PSADLSSQRG
KVFKLRNETH HLFVGLYPGT TYSFTIKAST AKGFGPPVTT RIATKISAPS MPEYDTDTPL
NETDTTITVM LKPAQSRGAP VSVYQLVVKE ERLQKSRRAA DIIECFSVPV SYRNASSLDS
LHYFAAELKP ANLPVTQPFT VGDNKTYNGY WNPPLSPLKS YSIYFQALSK ANGETKINCV
RLATKGASTQ NSNTVEPEKQ VDNTVKMAGV IAGLLMFIII LLGVMLTIKR RRNAYSYSYY
LKLAKKQKET QSGAQREMGP VASADKPTTK LSASRNDEGF SSSSQDVNGF TDGSRGELSQ
PTLTIQTHPY RTCDPVEMSY PRDQFQPAIR VADLLQHITQ MKRGQGYGFK EEYEALPEGQ
TASWDTAKED ENRNKNRYGN IISYDHSRVR LLVLDGDPHS DYINANYIDG YHRPRHYIAT
QGPMQETVKD FWRMIWQENS ASIVMVTNLV EVGRVKCVRY WPDDTEVYGD IKVTLIETEP
LAEYVIRTFT VQKKGYHEIR ELRLFHFTSW PDHGVPCYAT GLLGFVRQVK FLNPPEAGPI
VVHCSAGAGR TGCFIAIDTM LDMAENEGVV DIFNCVRELR AQRVNLVQTE EQYVFVHDAI
LEACLCGNTA IPVCEFRSLY YNISRLDPQT NSSQIKDEFQ TLNIVTPRVR PEDCSIGLLP
RNHDKNRSMD VLPLDRCLPF LISVDGESSN YINAALMDSH KQPAAFVVTQ HPLPNTVADF
WRLVFDYNCS SVVMLNEMDT AQFCMQYWPE KTSGCYGPIQ VEFVSADIDE DIIHRIFRIC
NMARPQDGYR IVQHLQYIGW PAYRDTPPSK RSLLKVVRRL EKWQEQYDGR EGRTVVHCLN
GGGRSGTFCA ICSVCEMIQQ QNIIDVFHIV KTLRNNKSNM VETLEQYKFV YEVALEYLSS
F*
mutated AA sequence MASLAALALS LLLRLQLPPL PGARAQSAPG GCSFDEHYSN CGYSVALGTN GFTWEQINTW
EKPMLDQAVP TGSFMMVNSS GRASGQKAHL LLPTLKENDT HCIDFHYYFS SRDRSSPGAL
NVYVKVNGGP QGNPVWNVSG VVTEGWVKAE LAISTFWPHF YQVIFESVSL KGHPGYIAVD
EVRVLAHPCR KAPHFLRLQN VEVNVGQNAT FQCIAGGKWS QHDKLWLQQW NGRDTALMVT
RVVNHRRFSA TVSVADTAQR SVSKYRCVIR SDGGSGVSNY AELIVKEPPT PIAPPELLAV
GATYLWIKPN ANSIIGDGPI ILKEVEYRTT TGTWAETHIV DSPNYKLWHL DPDVEYEIRV
LLTRPGEGGT GPPGPPLTTR TKCADPVHGP QNVEIVDIRA RQLTLQWEPF GYAVTRCHSY
NLTVQYQYVF NQQQYEAEEV IQTSSHYTLR GLRPFMTIRL RLLLSNPEGR MESEELVVQT
EEDVPGAVPL ESIQGGPFEE KIYIQWKPPN ETNGVITLYE INYKAVGSLD PSADLSSQRG
KVFKLRNETH HLFVGLYPGT TYSFTIKAST AKGFGPPVTT RIATKISAPS MPEYDTDTPL
NETDTTITVM LKPAQSRGAP VSVYQLVVKE ERLQKSRRAA DIIECFSVPV SYRNASSLDS
LHYFAAELKP ANLPVTQPFT VGDNKTYNGY WNPPLSPLKS YSIYFQALSK ANGETKINCV
RLATKGASTQ NSNTVEPEKQ VDNTVKMAGV IAGLLMFIII LLGVMLTIKR RRNAYSYSYY
LKLAKKQKET QSGAQREMGP VASADKPTTK LSASRNDEGF SSSSQDVNGF TDGSRGELSQ
PTLTIQTHPY RTCDPVEMSY PRDQFQPAIR VADLLQHITQ MKRGQGYGFK EEYEALPEGQ
TASWDTAKED ENRNKNRYGN IISYDHSRVR LLVLDGDPHS DYINANYIDG YHRPRHYIAT
QGPMQETVKD FWRMIWQENS ASIVMVTNLV EVGRVKCVRY WPDDTEVYGD IKVTLIETEP
LAEYVIRTFT VQKKGYHEIR ELRLFHFTSW PDHGVPCYAT GLLGFVRQVK FLNPPEAGPI
VVHCSAGAGR TGCFIAIDTM LDMAENEGVV DIFNCVRELR AQRVNLVQTE EQYVFVHDAI
LEACLCGNTA IPVCEFRSLY YNISRLDPQT NSSQIKDEFQ TLNIVTPRVR PEDCSIGLLP
RNHDKNRSMD VLPLDRCLPF LISVDGESSN YINAALMDSH KQPAAFVVTQ HPLPNTVADF
WRLVFDYNCS SVVMLNEMDT AQFCMQYWPE KTSGCYGPIQ VEFVSADIDE DIIHRIFRIC
NMARPQDGYR IVQHLQYIGW PAYRDTPPSK RSLLKVVRRL EKWQEQYDGR EGRTVVHCLN
GGGRSGTFCA ICSVCEMIQQ QNIIDVFHIV KTLRNNKSNM VETLEQYKFV YEVALEYLSS
F*
speed 1.05 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.887415891759721 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:41818289C>GN/A show variant in all transcripts   IGV
HGNC symbol PTPRT
Ensembl transcript ID ENST00000373193
Genbank transcript ID N/A
UniProt peptide O14522
alteration type single base exchange
alteration region CDS
DNA changes c.85G>C
cDNA.269G>C
g.322G>C
AA changes A29P Score: 27 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 29
frameshift no
known variant Reference ID: rs2867655
databasehomozygous (G/G)heterozygousallele carriers
1000G14287052133
ExAC583107690
regulatory features H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
Non-Gene Associated, Regulatory Feature, Non-Gene associated regulatory feature
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)1.8861
1.8861
(flanking)0.1471
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost325sequence motif lost- wt: GCAG|gtga
 mu: CCAG.gtga
Donor marginally increased324wt: 0.9951 / mu: 0.9960 (marginal change - not scored)wt: GCCGCAGGTGAGTGC
mu: GCCCCAGGTGAGTGC		 CGCA|ggtg
Donor gained3200.47mu: GAGCGCCCCAGGTGA GCGC|ccca
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      29PPLPGARAQSAAGGCSFDEHYSNC
mutated  not conserved    29PPLPGARAQSAPGGCSFDEHYSN
Ptroglodytes  all identical  ENSPTRG00000013505  29PPLPGARAQSAAGGCSFDEHYSN
Mmulatta  no alignment  ENSMMUG00000001108  n/a
Fcatus  no alignment  ENSFCAG00000004770  n/a
Mmusculus  all identical  ENSMUSG00000053141  29PPLPGAGAQSAAGGCSFDEHYSN
Ggallus  no alignment  ENSGALG00000003488  n/a
Trubripes  no alignment  ENSTRUG00000008419  n/a
Drerio  no alignment  ENSDARG00000074781  n/a
Dmelanogaster  no alignment  FBgn0014007  n/a
Celegans  no alignment  F56D1.4  n/a
Xtropicalis  no alignment  ENSXETG00000012126  n/a
protein features
start (aa)end (aa)featuredetails 
26747TOPO_DOMExtracellular (Potential).lost
30191DOMAINMAM.might get lost (downstream of altered splice site)
6060CONFLICTW -> T (in Ref. 1; AAD09421).might get lost (downstream of altered splice site)
7878CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
9898CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
137137CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
193284DOMAINIg-like C2-type.might get lost (downstream of altered splice site)
208208CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
213213DISULFIDBy similarity.might get lost (downstream of altered splice site)
267267DISULFIDBy similarity.might get lost (downstream of altered splice site)
288379DOMAINFibronectin type-III 1.might get lost (downstream of altered splice site)
375375CONFLICTP -> A (in Ref. 1; AAD09421).might get lost (downstream of altered splice site)
386480DOMAINFibronectin type-III 2.might get lost (downstream of altered splice site)
421421CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
481584DOMAINFibronectin type-III 3.might get lost (downstream of altered splice site)
510510CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
547547CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
589726DOMAINFibronectin type-III 4.might get lost (downstream of altered splice site)
601601CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
654654CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
684684CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
748768TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
7691441TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
867867CONFLICTP -> L (in Ref. 1; AAD09421).might get lost (downstream of altered splice site)
871873HELIXmight get lost (downstream of altered splice site)
874882HELIXmight get lost (downstream of altered splice site)
889895HELIXmight get lost (downstream of altered splice site)
8891143DOMAINTyrosine-protein phosphatase 1.might get lost (downstream of altered splice site)
905908TURNmight get lost (downstream of altered splice site)
910915HELIXmight get lost (downstream of altered splice site)
925927HELIXmight get lost (downstream of altered splice site)
938941HELIXmight get lost (downstream of altered splice site)
944948STRANDmight get lost (downstream of altered splice site)
951953STRANDmight get lost (downstream of altered splice site)
957960STRANDmight get lost (downstream of altered splice site)
965967TURNmight get lost (downstream of altered splice site)
968978HELIXmight get lost (downstream of altered splice site)
982985STRANDmight get lost (downstream of altered splice site)
989991STRANDmight get lost (downstream of altered splice site)
10031009STRANDmight get lost (downstream of altered splice site)
10111020STRANDmight get lost (downstream of altered splice site)
10221033STRANDmight get lost (downstream of altered splice site)
10401047STRANDmight get lost (downstream of altered splice site)
10521052BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
10601072HELIXmight get lost (downstream of altered splice site)
10801083STRANDmight get lost (downstream of altered splice site)
10841084ACT_SITEPhosphocysteine intermediate (By similarity).might get lost (downstream of altered splice site)
10841090REGIONSubstrate binding (By similarity).might get lost (downstream of altered splice site)
10851088STRANDmight get lost (downstream of altered splice site)
10891107HELIXmight get lost (downstream of altered splice site)
11081110STRANDmight get lost (downstream of altered splice site)
11121122HELIXmight get lost (downstream of altered splice site)
11281128BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
11301145HELIXmight get lost (downstream of altered splice site)
11751437DOMAINTyrosine-protein phosphatase 2.might get lost (downstream of altered splice site)
13781378ACT_SITEPhosphocysteine intermediate (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 4335 / 4335
position (AA) of stopcodon in wt / mu AA sequence 1445 / 1445
position of stopcodon in wt / mu cDNA 4519 / 4519
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 185 / 185
chromosome 20
strand -1
last intron/exon boundary 4466
theoretical NMD boundary in CDS 4231
length of CDS 4335
coding sequence (CDS) position 85
cDNA position
(for ins/del: last normal base / first normal base)		 269
gDNA position
(for ins/del: last normal base / first normal base)		 322
chromosomal position
(for ins/del: last normal base / first normal base)		 41818289
original gDNA sequence snippet GCGCCCGGGCTCAGAGCGCCGCAGGTGAGTGCGCCCGCCCG
altered gDNA sequence snippet GCGCCCGGGCTCAGAGCGCCCCAGGTGAGTGCGCCCGCCCG
original cDNA sequence snippet GCGCCCGGGCTCAGAGCGCCGCAGGTGGCTGTTCCTTTGAT
altered cDNA sequence snippet GCGCCCGGGCTCAGAGCGCCCCAGGTGGCTGTTCCTTTGAT
wildtype AA sequence MASLAALALS LLLRLQLPPL PGARAQSAAG GCSFDEHYSN CGYSVALGTN GFTWEQINTW
EKPMLDQAVP TGSFMMVNSS GRASGQKAHL LLPTLKENDT HCIDFHYYFS SRDRSSPGAL
NVYVKVNGGP QGNPVWNVSG VVTEGWVKAE LAISTFWPHF YQVIFESVSL KGHPGYIAVD
EVRVLAHPCR KAPHFLRLQN VEVNVGQNAT FQCIAGGKWS QHDKLWLQQW NGRDTALMVT
RVVNHRRFSA TVSVADTAQR SVSKYRCVIR SDGGSGVSNY AELIVKEPPT PIAPPELLAV
GATYLWIKPN ANSIIGDGPI ILKEVEYRTT TGTWAETHIV DSPNYKLWHL DPDVEYEIRV
LLTRPGEGGT GPPGPPLTTR TKCADPVHGP QNVEIVDIRA RQLTLQWEPF GYAVTRCHSY
NLTVQYQYVF NQQQYEAEEV IQTSSHYTLR GLRPFMTIRL RLLLSNPEGR MESEELVVQT
EEDVPGAVPL ESIQGGPFEE KIYIQWKPPN ETNGVITLYE INYKAVGSLD PSADLSSQRG
KVFKLRNETH HLFVGLYPGT TYSFTIKAST AKGFGPPVTT RIATKISAPS MPEYDTDTPL
NETDTTITVM LKPAQSRGAP VSVYQLVVKE ERLQKSRRAA DIIECFSVPV SYRNASSLDS
LHYFAAELKP ANLPVTQPFT VGDNKTYNGY WNPPLSPLKS YSIYFQALSK ANGETKINCV
RLATKGASTQ NSNTVEPEKQ VDNTVKMAGV IAGLLMFIII LLGVMLTIKR RRNAYSYSYY
LSQRKLAKKQ KETQSGAQRE MGPVASADKP TTKLSASRND EGFSSSSQDV NGFTDGSRGE
LSQPTLTIQT HPYRTCDPVE MSYPRDQFQP AIRVADLLQH ITQMKRGQGY GFKEEYEALP
EGQTASWDTA KEDENRNKNR YGNIISYDHS RVRLLVLDGD PHSDYINANY IDGYHRPRHY
IATQGPMQET VKDFWRMIWQ ENSASIVMVT NLVEVGRVKC VRYWPDDTEV YGDIKVTLIE
TEPLAEYVIR TFTVQKKGYH EIRELRLFHF TSWPDHGVPC YATGLLGFVR QVKFLNPPEA
GPIVVHCSAG AGRTGCFIAI DTMLDMAENE GVVDIFNCVR ELRAQRVNLV QTEEQYVFVH
DAILEACLCG NTAIPVCEFR SLYYNISRLD PQTNSSQIKD EFQTLNIVTP RVRPEDCSIG
LLPRNHDKNR SMDVLPLDRC LPFLISVDGE SSNYINAALM DSHKQPAAFV VTQHPLPNTV
ADFWRLVFDY NCSSVVMLNE MDTAQFCMQY WPEKTSGCYG PIQVEFVSAD IDEDIIHRIF
RICNMARPQD GYRIVQHLQY IGWPAYRDTP PSKRSLLKVV RRLEKWQEQY DGREGRTVVH
CLNGGGRSGT FCAICSVCEM IQQQNIIDVF HIVKTLRNNK SNMVETLEQY KFVYEVALEY
LSSF*
mutated AA sequence MASLAALALS LLLRLQLPPL PGARAQSAPG GCSFDEHYSN CGYSVALGTN GFTWEQINTW
EKPMLDQAVP TGSFMMVNSS GRASGQKAHL LLPTLKENDT HCIDFHYYFS SRDRSSPGAL
NVYVKVNGGP QGNPVWNVSG VVTEGWVKAE LAISTFWPHF YQVIFESVSL KGHPGYIAVD
EVRVLAHPCR KAPHFLRLQN VEVNVGQNAT FQCIAGGKWS QHDKLWLQQW NGRDTALMVT
RVVNHRRFSA TVSVADTAQR SVSKYRCVIR SDGGSGVSNY AELIVKEPPT PIAPPELLAV
GATYLWIKPN ANSIIGDGPI ILKEVEYRTT TGTWAETHIV DSPNYKLWHL DPDVEYEIRV
LLTRPGEGGT GPPGPPLTTR TKCADPVHGP QNVEIVDIRA RQLTLQWEPF GYAVTRCHSY
NLTVQYQYVF NQQQYEAEEV IQTSSHYTLR GLRPFMTIRL RLLLSNPEGR MESEELVVQT
EEDVPGAVPL ESIQGGPFEE KIYIQWKPPN ETNGVITLYE INYKAVGSLD PSADLSSQRG
KVFKLRNETH HLFVGLYPGT TYSFTIKAST AKGFGPPVTT RIATKISAPS MPEYDTDTPL
NETDTTITVM LKPAQSRGAP VSVYQLVVKE ERLQKSRRAA DIIECFSVPV SYRNASSLDS
LHYFAAELKP ANLPVTQPFT VGDNKTYNGY WNPPLSPLKS YSIYFQALSK ANGETKINCV
RLATKGASTQ NSNTVEPEKQ VDNTVKMAGV IAGLLMFIII LLGVMLTIKR RRNAYSYSYY
LSQRKLAKKQ KETQSGAQRE MGPVASADKP TTKLSASRND EGFSSSSQDV NGFTDGSRGE
LSQPTLTIQT HPYRTCDPVE MSYPRDQFQP AIRVADLLQH ITQMKRGQGY GFKEEYEALP
EGQTASWDTA KEDENRNKNR YGNIISYDHS RVRLLVLDGD PHSDYINANY IDGYHRPRHY
IATQGPMQET VKDFWRMIWQ ENSASIVMVT NLVEVGRVKC VRYWPDDTEV YGDIKVTLIE
TEPLAEYVIR TFTVQKKGYH EIRELRLFHF TSWPDHGVPC YATGLLGFVR QVKFLNPPEA
GPIVVHCSAG AGRTGCFIAI DTMLDMAENE GVVDIFNCVR ELRAQRVNLV QTEEQYVFVH
DAILEACLCG NTAIPVCEFR SLYYNISRLD PQTNSSQIKD EFQTLNIVTP RVRPEDCSIG
LLPRNHDKNR SMDVLPLDRC LPFLISVDGE SSNYINAALM DSHKQPAAFV VTQHPLPNTV
ADFWRLVFDY NCSSVVMLNE MDTAQFCMQY WPEKTSGCYG PIQVEFVSAD IDEDIIHRIF
RICNMARPQD GYRIVQHLQY IGWPAYRDTP PSKRSLLKVV RRLEKWQEQY DGREGRTVVH
CLNGGGRSGT FCAICSVCEM IQQQNIIDVF HIVKTLRNNK SNMVETLEQY KFVYEVALEY
LSSF*
speed 0.49 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.887415891759721 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:41818289C>GN/A show variant in all transcripts   IGV
HGNC symbol PTPRT
Ensembl transcript ID ENST00000356100
Genbank transcript ID N/A
UniProt peptide O14522
alteration type single base exchange
alteration region CDS
DNA changes c.85G>C
cDNA.85G>C
g.322G>C
AA changes A29P Score: 27 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 29
frameshift no
known variant Reference ID: rs2867655
databasehomozygous (G/G)heterozygousallele carriers
1000G14287052133
ExAC583107690
regulatory features H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
Non-Gene Associated, Regulatory Feature, Non-Gene associated regulatory feature
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)1.8861
1.8861
(flanking)0.1471
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost325sequence motif lost- wt: GCAG|gtga
 mu: CCAG.gtga
Donor marginally increased324wt: 0.9951 / mu: 0.9960 (marginal change - not scored)wt: GCCGCAGGTGAGTGC
mu: GCCCCAGGTGAGTGC		 CGCA|ggtg
Donor gained3200.47mu: GAGCGCCCCAGGTGA GCGC|ccca
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      29PPLPGARAQSAAGGCSFDEHYSNC
mutated  not conserved    29PPLPGARAQSAPGGCSFDEHYSN
Ptroglodytes  all identical  ENSPTRG00000013505  29PPLPGARAQSAAGGCSFDEHYSN
Mmulatta  no alignment  ENSMMUG00000001108  n/a
Fcatus  no alignment  ENSFCAG00000004770  n/a
Mmusculus  all identical  ENSMUSG00000053141  29PPLPGAGAQSAAGGCSFDEHYSN
Ggallus  no alignment  ENSGALG00000003488  n/a
Trubripes  no alignment  ENSTRUG00000008419  n/a
Drerio  no alignment  ENSDARG00000074781  n/a
Dmelanogaster  no alignment  FBgn0014007  n/a
Celegans  no alignment  F56D1.4  n/a
Xtropicalis  no alignment  ENSXETG00000012126  n/a
protein features
start (aa)end (aa)featuredetails 
26747TOPO_DOMExtracellular (Potential).lost
30191DOMAINMAM.might get lost (downstream of altered splice site)
6060CONFLICTW -> T (in Ref. 1; AAD09421).might get lost (downstream of altered splice site)
7878CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
9898CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
137137CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
193284DOMAINIg-like C2-type.might get lost (downstream of altered splice site)
208208CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
213213DISULFIDBy similarity.might get lost (downstream of altered splice site)
267267DISULFIDBy similarity.might get lost (downstream of altered splice site)
288379DOMAINFibronectin type-III 1.might get lost (downstream of altered splice site)
375375CONFLICTP -> A (in Ref. 1; AAD09421).might get lost (downstream of altered splice site)
386480DOMAINFibronectin type-III 2.might get lost (downstream of altered splice site)
421421CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
481584DOMAINFibronectin type-III 3.might get lost (downstream of altered splice site)
510510CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
547547CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
589726DOMAINFibronectin type-III 4.might get lost (downstream of altered splice site)
601601CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
654654CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
684684CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
748768TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
7691441TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
867867CONFLICTP -> L (in Ref. 1; AAD09421).might get lost (downstream of altered splice site)
871873HELIXmight get lost (downstream of altered splice site)
874882HELIXmight get lost (downstream of altered splice site)
889895HELIXmight get lost (downstream of altered splice site)
8891143DOMAINTyrosine-protein phosphatase 1.might get lost (downstream of altered splice site)
905908TURNmight get lost (downstream of altered splice site)
910915HELIXmight get lost (downstream of altered splice site)
925927HELIXmight get lost (downstream of altered splice site)
938941HELIXmight get lost (downstream of altered splice site)
944948STRANDmight get lost (downstream of altered splice site)
951953STRANDmight get lost (downstream of altered splice site)
957960STRANDmight get lost (downstream of altered splice site)
965967TURNmight get lost (downstream of altered splice site)
968978HELIXmight get lost (downstream of altered splice site)
982985STRANDmight get lost (downstream of altered splice site)
989991STRANDmight get lost (downstream of altered splice site)
10031009STRANDmight get lost (downstream of altered splice site)
10111020STRANDmight get lost (downstream of altered splice site)
10221033STRANDmight get lost (downstream of altered splice site)
10401047STRANDmight get lost (downstream of altered splice site)
10521052BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
10601072HELIXmight get lost (downstream of altered splice site)
10801083STRANDmight get lost (downstream of altered splice site)
10841084ACT_SITEPhosphocysteine intermediate (By similarity).might get lost (downstream of altered splice site)
10841090REGIONSubstrate binding (By similarity).might get lost (downstream of altered splice site)
10851088STRANDmight get lost (downstream of altered splice site)
10891107HELIXmight get lost (downstream of altered splice site)
11081110STRANDmight get lost (downstream of altered splice site)
11121122HELIXmight get lost (downstream of altered splice site)
11281128BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
11301145HELIXmight get lost (downstream of altered splice site)
11751437DOMAINTyrosine-protein phosphatase 2.might get lost (downstream of altered splice site)
13781378ACT_SITEPhosphocysteine intermediate (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 4353 / 4353
position (AA) of stopcodon in wt / mu AA sequence 1451 / 1451
position of stopcodon in wt / mu cDNA 4353 / 4353
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 1 / 1
chromosome 20
strand -1
last intron/exon boundary 4300
theoretical NMD boundary in CDS 4249
length of CDS 4353
coding sequence (CDS) position 85
cDNA position
(for ins/del: last normal base / first normal base)		 85
gDNA position
(for ins/del: last normal base / first normal base)		 322
chromosomal position
(for ins/del: last normal base / first normal base)		 41818289
original gDNA sequence snippet GCGCCCGGGCTCAGAGCGCCGCAGGTGAGTGCGCCCGCCCG
altered gDNA sequence snippet GCGCCCGGGCTCAGAGCGCCCCAGGTGAGTGCGCCCGCCCG
original cDNA sequence snippet GCGCCCGGGCTCAGAGCGCCGCAGGTGGCTGTTCCTTTGAT
altered cDNA sequence snippet GCGCCCGGGCTCAGAGCGCCCCAGGTGGCTGTTCCTTTGAT
wildtype AA sequence MASLAALALS LLLRLQLPPL PGARAQSAAG GCSFDEHYSN CGYSVALGTN GFTWEQINTW
EKPMLDQAVP TGSFMMVNSS GRASGQKAHL LLPTLKENDT HCIDFHYYFS SRDRSSPGAL
NVYVKVNGGP QGNPVWNVSG VVTEGWVKAE LAISTFWPHF YQVIFESVSL KGHPGYIAVD
EVRVLAHPCR KAPHFLRLQN VEVNVGQNAT FQCIAGGKWS QHDKLWLQQW NGRDTALMVT
RVVNHRRFSA TVSVADTAQR SVSKYRCVIR SDGGSGVSNY AELIVKEPPT PIAPPELLAV
GATYLWIKPN ANSIIGDGPI ILKEVEYRTT TGTWAETHIV DSPNYKLWHL DPDVEYEIRV
LLTRPGEGGT GPPGPPLTTR TKCADPVHGP QNVEIVDIRA RQLTLQWEPF GYAVTRCHSY
NLTVQYQYVF NQQQYEAEEV IQTSSHYTLR GLRPFMTIRL RLLLSNPEGR MESEELVVQT
EEDVPGAVPL ESIQGGPFEE KIYIQWKPPN ETNGVITLYE INYKAVGSLD PSADLSSQRG
KVFKLRNETH HLFVGLYPGT TYSFTIKAST AKGFGPPVTT RIATKISAPS MPEYDTDTPL
NETDTTITVM LKPAQSRGAP VSVYQLVVKE ERLQKSRRAA DIIECFSVPV SYRNASSLDS
LHYFAAELKP ANLPVTQPFT VGDNKTYNGY WNPPLSPLKS YSIYFQALSK ANGETKINCV
RLATKAPMGS AQVTPGTPLC LLTTGASTQN SNTVEPEKQV DNTVKMAGVI AGLLMFIIIL
LGVMLTIKRR KLAKKQKETQ SGAQREMGPV ASADKPTTKL SASRNDEGFS SSSQDVNGFT
DGSRGELSQP TLTIQTHPYR TCDPVEMSYP RDQFQPAIRV ADLLQHITQM KRGQGYGFKE
EYEALPEGQT ASWDTAKEDE NRNKNRYGNI ISYDHSRVRL LVLDGDPHSD YINANYIDGY
HRPRHYIATQ GPMQETVKDF WRMIWQENSA SIVMVTNLVE VGRVKCVRYW PDDTEVYGDI
KVTLIETEPL AEYVIRTFTV QKKGYHEIRE LRLFHFTSWP DHGVPCYATG LLGFVRQVKF
LNPPEAGPIV VHCSAGAGRT GCFIAIDTML DMAENEGVVD IFNCVRELRA QRVNLVQTEE
QYVFVHDAIL EACLCGNTAI PVCEFRSLYY NISRLDPQTN SSQIKDEFQT LNIVTPRVRP
EDCSIGLLPR NHDKNRSMDV LPLDRCLPFL ISVDGESSNY INAALMDSHK QPAAFVVTQH
PLPNTVADFW RLVFDYNCSS VVMLNEMDTA QFCMQYWPEK TSGCYGPIQV EFVSADIDED
IIHRIFRICN MARPQDGYRI VQHLQYIGWP AYRDTPPSKR SLLKVVRRLE KWQEQYDGRE
GRTVVHCLNG GGRSGTFCAI CSVCEMIQQQ NIIDVFHIVK TLRNNKSNMV ETLEQYKFVY
EVALEYLSSF *
mutated AA sequence MASLAALALS LLLRLQLPPL PGARAQSAPG GCSFDEHYSN CGYSVALGTN GFTWEQINTW
EKPMLDQAVP TGSFMMVNSS GRASGQKAHL LLPTLKENDT HCIDFHYYFS SRDRSSPGAL
NVYVKVNGGP QGNPVWNVSG VVTEGWVKAE LAISTFWPHF YQVIFESVSL KGHPGYIAVD
EVRVLAHPCR KAPHFLRLQN VEVNVGQNAT FQCIAGGKWS QHDKLWLQQW NGRDTALMVT
RVVNHRRFSA TVSVADTAQR SVSKYRCVIR SDGGSGVSNY AELIVKEPPT PIAPPELLAV
GATYLWIKPN ANSIIGDGPI ILKEVEYRTT TGTWAETHIV DSPNYKLWHL DPDVEYEIRV
LLTRPGEGGT GPPGPPLTTR TKCADPVHGP QNVEIVDIRA RQLTLQWEPF GYAVTRCHSY
NLTVQYQYVF NQQQYEAEEV IQTSSHYTLR GLRPFMTIRL RLLLSNPEGR MESEELVVQT
EEDVPGAVPL ESIQGGPFEE KIYIQWKPPN ETNGVITLYE INYKAVGSLD PSADLSSQRG
KVFKLRNETH HLFVGLYPGT TYSFTIKAST AKGFGPPVTT RIATKISAPS MPEYDTDTPL
NETDTTITVM LKPAQSRGAP VSVYQLVVKE ERLQKSRRAA DIIECFSVPV SYRNASSLDS
LHYFAAELKP ANLPVTQPFT VGDNKTYNGY WNPPLSPLKS YSIYFQALSK ANGETKINCV
RLATKAPMGS AQVTPGTPLC LLTTGASTQN SNTVEPEKQV DNTVKMAGVI AGLLMFIIIL
LGVMLTIKRR KLAKKQKETQ SGAQREMGPV ASADKPTTKL SASRNDEGFS SSSQDVNGFT
DGSRGELSQP TLTIQTHPYR TCDPVEMSYP RDQFQPAIRV ADLLQHITQM KRGQGYGFKE
EYEALPEGQT ASWDTAKEDE NRNKNRYGNI ISYDHSRVRL LVLDGDPHSD YINANYIDGY
HRPRHYIATQ GPMQETVKDF WRMIWQENSA SIVMVTNLVE VGRVKCVRYW PDDTEVYGDI
KVTLIETEPL AEYVIRTFTV QKKGYHEIRE LRLFHFTSWP DHGVPCYATG LLGFVRQVKF
LNPPEAGPIV VHCSAGAGRT GCFIAIDTML DMAENEGVVD IFNCVRELRA QRVNLVQTEE
QYVFVHDAIL EACLCGNTAI PVCEFRSLYY NISRLDPQTN SSQIKDEFQT LNIVTPRVRP
EDCSIGLLPR NHDKNRSMDV LPLDRCLPFL ISVDGESSNY INAALMDSHK QPAAFVVTQH
PLPNTVADFW RLVFDYNCSS VVMLNEMDTA QFCMQYWPEK TSGCYGPIQV EFVSADIDED
IIHRIFRICN MARPQDGYRI VQHLQYIGWP AYRDTPPSKR SLLKVVRRLE KWQEQYDGRE
GRTVVHCLNG GGRSGTFCAI CSVCEMIQQQ NIIDVFHIVK TLRNNKSNMV ETLEQYKFVY
EVALEYLSSF *
speed 0.41 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.887415891759721 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:41818289C>GN/A show variant in all transcripts   IGV
HGNC symbol PTPRT
Ensembl transcript ID ENST00000373198
Genbank transcript ID NM_133170
UniProt peptide O14522
alteration type single base exchange
alteration region CDS
DNA changes c.85G>C
cDNA.321G>C
g.322G>C
AA changes A29P Score: 27 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 29
frameshift no
known variant Reference ID: rs2867655
databasehomozygous (G/G)heterozygousallele carriers
1000G14287052133
ExAC583107690
regulatory features H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
Non-Gene Associated, Regulatory Feature, Non-Gene associated regulatory feature
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)1.8861
1.8861
(flanking)0.1471
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost325sequence motif lost- wt: GCAG|gtga
 mu: CCAG.gtga
Donor marginally increased324wt: 0.9951 / mu: 0.9960 (marginal change - not scored)wt: GCCGCAGGTGAGTGC
mu: GCCCCAGGTGAGTGC		 CGCA|ggtg
Donor gained3200.47mu: GAGCGCCCCAGGTGA GCGC|ccca
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      29PPLPGARAQSAAGGCSFDEHYSNC
mutated  not conserved    29PPLPGARAQSAPGGCSFDEHYSN
Ptroglodytes  all identical  ENSPTRG00000013505  29PPLPGARAQSAAGGCSFDEHYSN
Mmulatta  no alignment  ENSMMUG00000001108  n/a
Fcatus  no alignment  ENSFCAG00000004770  n/a
Mmusculus  all identical  ENSMUSG00000053141  29PPLPGAGAQSAAGGCSFDEHYSN
Ggallus  no alignment  ENSGALG00000003488  n/a
Trubripes  no alignment  ENSTRUG00000008419  n/a
Drerio  no alignment  ENSDARG00000074781  n/a
Dmelanogaster  no alignment  FBgn0014007  n/a
Celegans  no alignment  F56D1.4  n/a
Xtropicalis  no alignment  ENSXETG00000012126  n/a
protein features
start (aa)end (aa)featuredetails 
26747TOPO_DOMExtracellular (Potential).lost
30191DOMAINMAM.might get lost (downstream of altered splice site)
6060CONFLICTW -> T (in Ref. 1; AAD09421).might get lost (downstream of altered splice site)
7878CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
9898CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
137137CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
193284DOMAINIg-like C2-type.might get lost (downstream of altered splice site)
208208CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
213213DISULFIDBy similarity.might get lost (downstream of altered splice site)
267267DISULFIDBy similarity.might get lost (downstream of altered splice site)
288379DOMAINFibronectin type-III 1.might get lost (downstream of altered splice site)
375375CONFLICTP -> A (in Ref. 1; AAD09421).might get lost (downstream of altered splice site)
386480DOMAINFibronectin type-III 2.might get lost (downstream of altered splice site)
421421CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
481584DOMAINFibronectin type-III 3.might get lost (downstream of altered splice site)
510510CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
547547CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
589726DOMAINFibronectin type-III 4.might get lost (downstream of altered splice site)
601601CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
654654CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
684684CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
748768TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
7691441TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
867867CONFLICTP -> L (in Ref. 1; AAD09421).might get lost (downstream of altered splice site)
871873HELIXmight get lost (downstream of altered splice site)
874882HELIXmight get lost (downstream of altered splice site)
889895HELIXmight get lost (downstream of altered splice site)
8891143DOMAINTyrosine-protein phosphatase 1.might get lost (downstream of altered splice site)
905908TURNmight get lost (downstream of altered splice site)
910915HELIXmight get lost (downstream of altered splice site)
925927HELIXmight get lost (downstream of altered splice site)
938941HELIXmight get lost (downstream of altered splice site)
944948STRANDmight get lost (downstream of altered splice site)
951953STRANDmight get lost (downstream of altered splice site)
957960STRANDmight get lost (downstream of altered splice site)
965967TURNmight get lost (downstream of altered splice site)
968978HELIXmight get lost (downstream of altered splice site)
982985STRANDmight get lost (downstream of altered splice site)
989991STRANDmight get lost (downstream of altered splice site)
10031009STRANDmight get lost (downstream of altered splice site)
10111020STRANDmight get lost (downstream of altered splice site)
10221033STRANDmight get lost (downstream of altered splice site)
10401047STRANDmight get lost (downstream of altered splice site)
10521052BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
10601072HELIXmight get lost (downstream of altered splice site)
10801083STRANDmight get lost (downstream of altered splice site)
10841084ACT_SITEPhosphocysteine intermediate (By similarity).might get lost (downstream of altered splice site)
10841090REGIONSubstrate binding (By similarity).might get lost (downstream of altered splice site)
10851088STRANDmight get lost (downstream of altered splice site)
10891107HELIXmight get lost (downstream of altered splice site)
11081110STRANDmight get lost (downstream of altered splice site)
11121122HELIXmight get lost (downstream of altered splice site)
11281128BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
11301145HELIXmight get lost (downstream of altered splice site)
11751437DOMAINTyrosine-protein phosphatase 2.might get lost (downstream of altered splice site)
13781378ACT_SITEPhosphocysteine intermediate (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 4392 / 4392
position (AA) of stopcodon in wt / mu AA sequence 1464 / 1464
position of stopcodon in wt / mu cDNA 4628 / 4628
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 237 / 237
chromosome 20
strand -1
last intron/exon boundary 4575
theoretical NMD boundary in CDS 4288
length of CDS 4392
coding sequence (CDS) position 85
cDNA position
(for ins/del: last normal base / first normal base)		 321
gDNA position
(for ins/del: last normal base / first normal base)		 322
chromosomal position
(for ins/del: last normal base / first normal base)		 41818289
original gDNA sequence snippet GCGCCCGGGCTCAGAGCGCCGCAGGTGAGTGCGCCCGCCCG
altered gDNA sequence snippet GCGCCCGGGCTCAGAGCGCCCCAGGTGAGTGCGCCCGCCCG
original cDNA sequence snippet GCGCCCGGGCTCAGAGCGCCGCAGGTGGCTGTTCCTTTGAT
altered cDNA sequence snippet GCGCCCGGGCTCAGAGCGCCCCAGGTGGCTGTTCCTTTGAT
wildtype AA sequence MASLAALALS LLLRLQLPPL PGARAQSAAG GCSFDEHYSN CGYSVALGTN GFTWEQINTW
EKPMLDQAVP TGSFMMVNSS GRASGQKAHL LLPTLKENDT HCIDFHYYFS SRDRSSPGAL
NVYVKVNGGP QGNPVWNVSG VVTEGWVKAE LAISTFWPHF YQVIFESVSL KGHPGYIAVD
EVRVLAHPCR KAPHFLRLQN VEVNVGQNAT FQCIAGGKWS QHDKLWLQQW NGRDTALMVT
RVVNHRRFSA TVSVADTAQR SVSKYRCVIR SDGGSGVSNY AELIVKEPPT PIAPPELLAV
GATYLWIKPN ANSIIGDGPI ILKEVEYRTT TGTWAETHIV DSPNYKLWHL DPDVEYEIRV
LLTRPGEGGT GPPGPPLTTR TKCADPVHGP QNVEIVDIRA RQLTLQWEPF GYAVTRCHSY
NLTVQYQYVF NQQQYEAEEV IQTSSHYTLR GLRPFMTIRL RLLLSNPEGR MESEELVVQT
EEDVPGAVPL ESIQGGPFEE KIYIQWKPPN ETNGVITLYE INYKAVGSLD PSADLSSQRG
KVFKLRNETH HLFVGLYPGT TYSFTIKAST AKGFGPPVTT RIATKISAPS MPEYDTDTPL
NETDTTITVM LKPAQSRGAP VSVYQLVVKE ERLQKSRRAA DIIECFSVPV SYRNASSLDS
LHYFAAELKP ANLPVTQPFT VGDNKTYNGY WNPPLSPLKS YSIYFQALSK ANGETKINCV
RLATKAPMGS AQVTPGTPLC LLTTGASTQN SNTVEPEKQV DNTVKMAGVI AGLLMFIIIL
LGVMLTIKRR RNAYSYSYYL SQRKLAKKQK ETQSGAQREM GPVASADKPT TKLSASRNDE
GFSSSSQDVN GFTDGSRGEL SQPTLTIQTH PYRTCDPVEM SYPRDQFQPA IRVADLLQHI
TQMKRGQGYG FKEEYEALPE GQTASWDTAK EDENRNKNRY GNIISYDHSR VRLLVLDGDP
HSDYINANYI DGYHRPRHYI ATQGPMQETV KDFWRMIWQE NSASIVMVTN LVEVGRVKCV
RYWPDDTEVY GDIKVTLIET EPLAEYVIRT FTVQKKGYHE IRELRLFHFT SWPDHGVPCY
ATGLLGFVRQ VKFLNPPEAG PIVVHCSAGA GRTGCFIAID TMLDMAENEG VVDIFNCVRE
LRAQRVNLVQ TEEQYVFVHD AILEACLCGN TAIPVCEFRS LYYNISRLDP QTNSSQIKDE
FQTLNIVTPR VRPEDCSIGL LPRNHDKNRS MDVLPLDRCL PFLISVDGES SNYINAALMD
SHKQPAAFVV TQHPLPNTVA DFWRLVFDYN CSSVVMLNEM DTAQFCMQYW PEKTSGCYGP
IQVEFVSADI DEDIIHRIFR ICNMARPQDG YRIVQHLQYI GWPAYRDTPP SKRSLLKVVR
RLEKWQEQYD GREGRTVVHC LNGGGRSGTF CAICSVCEMI QQQNIIDVFH IVKTLRNNKS
NMVETLEQYK FVYEVALEYL SSF*
mutated AA sequence MASLAALALS LLLRLQLPPL PGARAQSAPG GCSFDEHYSN CGYSVALGTN GFTWEQINTW
EKPMLDQAVP TGSFMMVNSS GRASGQKAHL LLPTLKENDT HCIDFHYYFS SRDRSSPGAL
NVYVKVNGGP QGNPVWNVSG VVTEGWVKAE LAISTFWPHF YQVIFESVSL KGHPGYIAVD
EVRVLAHPCR KAPHFLRLQN VEVNVGQNAT FQCIAGGKWS QHDKLWLQQW NGRDTALMVT
RVVNHRRFSA TVSVADTAQR SVSKYRCVIR SDGGSGVSNY AELIVKEPPT PIAPPELLAV
GATYLWIKPN ANSIIGDGPI ILKEVEYRTT TGTWAETHIV DSPNYKLWHL DPDVEYEIRV
LLTRPGEGGT GPPGPPLTTR TKCADPVHGP QNVEIVDIRA RQLTLQWEPF GYAVTRCHSY
NLTVQYQYVF NQQQYEAEEV IQTSSHYTLR GLRPFMTIRL RLLLSNPEGR MESEELVVQT
EEDVPGAVPL ESIQGGPFEE KIYIQWKPPN ETNGVITLYE INYKAVGSLD PSADLSSQRG
KVFKLRNETH HLFVGLYPGT TYSFTIKAST AKGFGPPVTT RIATKISAPS MPEYDTDTPL
NETDTTITVM LKPAQSRGAP VSVYQLVVKE ERLQKSRRAA DIIECFSVPV SYRNASSLDS
LHYFAAELKP ANLPVTQPFT VGDNKTYNGY WNPPLSPLKS YSIYFQALSK ANGETKINCV
RLATKAPMGS AQVTPGTPLC LLTTGASTQN SNTVEPEKQV DNTVKMAGVI AGLLMFIIIL
LGVMLTIKRR RNAYSYSYYL SQRKLAKKQK ETQSGAQREM GPVASADKPT TKLSASRNDE
GFSSSSQDVN GFTDGSRGEL SQPTLTIQTH PYRTCDPVEM SYPRDQFQPA IRVADLLQHI
TQMKRGQGYG FKEEYEALPE GQTASWDTAK EDENRNKNRY GNIISYDHSR VRLLVLDGDP
HSDYINANYI DGYHRPRHYI ATQGPMQETV KDFWRMIWQE NSASIVMVTN LVEVGRVKCV
RYWPDDTEVY GDIKVTLIET EPLAEYVIRT FTVQKKGYHE IRELRLFHFT SWPDHGVPCY
ATGLLGFVRQ VKFLNPPEAG PIVVHCSAGA GRTGCFIAID TMLDMAENEG VVDIFNCVRE
LRAQRVNLVQ TEEQYVFVHD AILEACLCGN TAIPVCEFRS LYYNISRLDP QTNSSQIKDE
FQTLNIVTPR VRPEDCSIGL LPRNHDKNRS MDVLPLDRCL PFLISVDGES SNYINAALMD
SHKQPAAFVV TQHPLPNTVA DFWRLVFDYN CSSVVMLNEM DTAQFCMQYW PEKTSGCYGP
IQVEFVSADI DEDIIHRIFR ICNMARPQDG YRIVQHLQYI GWPAYRDTPP SKRSLLKVVR
RLEKWQEQYD GREGRTVVHC LNGGGRSGTF CAICSVCEMI QQQNIIDVFH IVKTLRNNKS
NMVETLEQYK FVYEVALEYL SSF*
speed 1.00 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.887415891759721 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:41818289C>GN/A show variant in all transcripts   IGV
HGNC symbol PTPRT
Ensembl transcript ID ENST00000373184
Genbank transcript ID N/A
UniProt peptide O14522
alteration type single base exchange
alteration region CDS
DNA changes c.85G>C
cDNA.85G>C
g.322G>C
AA changes A29P Score: 27 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 29
frameshift no
known variant Reference ID: rs2867655
databasehomozygous (G/G)heterozygousallele carriers
1000G14287052133
ExAC583107690
regulatory features H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
Non-Gene Associated, Regulatory Feature, Non-Gene associated regulatory feature
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)1.8861
1.8861
(flanking)0.1471
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost325sequence motif lost- wt: GCAG|gtga
 mu: CCAG.gtga
Donor marginally increased324wt: 0.9951 / mu: 0.9960 (marginal change - not scored)wt: GCCGCAGGTGAGTGC
mu: GCCCCAGGTGAGTGC		 CGCA|ggtg
Donor gained3200.47mu: GAGCGCCCCAGGTGA GCGC|ccca
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      29PPLPGARAQSAAGGCSFDEHYSNC
mutated  not conserved    29PPLPGARAQSAPGGCSFDEHYSN
Ptroglodytes  all identical  ENSPTRG00000013505  29PPLPGARAQSAAGGCSFDEHYSN
Mmulatta  no alignment  ENSMMUG00000001108  n/a
Fcatus  no alignment  ENSFCAG00000004770  n/a
Mmusculus  all identical  ENSMUSG00000053141  29PPLPGAGAQSAAGGCSFDEHYSN
Ggallus  no alignment  ENSGALG00000003488  n/a
Trubripes  no alignment  ENSTRUG00000008419  n/a
Drerio  no alignment  ENSDARG00000074781  n/a
Dmelanogaster  no alignment  FBgn0014007  n/a
Celegans  no alignment  F56D1.4  n/a
Xtropicalis  no alignment  ENSXETG00000012126  n/a
protein features
start (aa)end (aa)featuredetails 
26747TOPO_DOMExtracellular (Potential).lost
30191DOMAINMAM.might get lost (downstream of altered splice site)
6060CONFLICTW -> T (in Ref. 1; AAD09421).might get lost (downstream of altered splice site)
7878CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
9898CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
137137CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
193284DOMAINIg-like C2-type.might get lost (downstream of altered splice site)
208208CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
213213DISULFIDBy similarity.might get lost (downstream of altered splice site)
267267DISULFIDBy similarity.might get lost (downstream of altered splice site)
288379DOMAINFibronectin type-III 1.might get lost (downstream of altered splice site)
375375CONFLICTP -> A (in Ref. 1; AAD09421).might get lost (downstream of altered splice site)
386480DOMAINFibronectin type-III 2.might get lost (downstream of altered splice site)
421421CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
481584DOMAINFibronectin type-III 3.might get lost (downstream of altered splice site)
510510CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
547547CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
589726DOMAINFibronectin type-III 4.might get lost (downstream of altered splice site)
601601CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
654654CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
684684CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
748768TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
7691441TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
867867CONFLICTP -> L (in Ref. 1; AAD09421).might get lost (downstream of altered splice site)
871873HELIXmight get lost (downstream of altered splice site)
874882HELIXmight get lost (downstream of altered splice site)
889895HELIXmight get lost (downstream of altered splice site)
8891143DOMAINTyrosine-protein phosphatase 1.might get lost (downstream of altered splice site)
905908TURNmight get lost (downstream of altered splice site)
910915HELIXmight get lost (downstream of altered splice site)
925927HELIXmight get lost (downstream of altered splice site)
938941HELIXmight get lost (downstream of altered splice site)
944948STRANDmight get lost (downstream of altered splice site)
951953STRANDmight get lost (downstream of altered splice site)
957960STRANDmight get lost (downstream of altered splice site)
965967TURNmight get lost (downstream of altered splice site)
968978HELIXmight get lost (downstream of altered splice site)
982985STRANDmight get lost (downstream of altered splice site)
989991STRANDmight get lost (downstream of altered splice site)
10031009STRANDmight get lost (downstream of altered splice site)
10111020STRANDmight get lost (downstream of altered splice site)
10221033STRANDmight get lost (downstream of altered splice site)
10401047STRANDmight get lost (downstream of altered splice site)
10521052BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
10601072HELIXmight get lost (downstream of altered splice site)
10801083STRANDmight get lost (downstream of altered splice site)
10841084ACT_SITEPhosphocysteine intermediate (By similarity).might get lost (downstream of altered splice site)
10841090REGIONSubstrate binding (By similarity).might get lost (downstream of altered splice site)
10851088STRANDmight get lost (downstream of altered splice site)
10891107HELIXmight get lost (downstream of altered splice site)
11081110STRANDmight get lost (downstream of altered splice site)
11121122HELIXmight get lost (downstream of altered splice site)
11281128BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
11301145HELIXmight get lost (downstream of altered splice site)
11751437DOMAINTyrosine-protein phosphatase 2.might get lost (downstream of altered splice site)
13781378ACT_SITEPhosphocysteine intermediate (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 4356 / 4356
position (AA) of stopcodon in wt / mu AA sequence 1452 / 1452
position of stopcodon in wt / mu cDNA 4356 / 4356
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 1 / 1
chromosome 20
strand -1
last intron/exon boundary 4303
theoretical NMD boundary in CDS 4252
length of CDS 4356
coding sequence (CDS) position 85
cDNA position
(for ins/del: last normal base / first normal base)		 85
gDNA position
(for ins/del: last normal base / first normal base)		 322
chromosomal position
(for ins/del: last normal base / first normal base)		 41818289
original gDNA sequence snippet GCGCCCGGGCTCAGAGCGCCGCAGGTGAGTGCGCCCGCCCG
altered gDNA sequence snippet GCGCCCGGGCTCAGAGCGCCCCAGGTGAGTGCGCCCGCCCG
original cDNA sequence snippet GCGCCCGGGCTCAGAGCGCCGCAGGTGGCTGTTCCTTTGAT
altered cDNA sequence snippet GCGCCCGGGCTCAGAGCGCCCCAGGTGGCTGTTCCTTTGAT
wildtype AA sequence MASLAALALS LLLRLQLPPL PGARAQSAAG GCSFDEHYSN CGYSVALGTN GFTWEQINTW
EKPMLDQAVP TGSFMMVNSS GRASGQKAHL LLPTLKENDT HCIDFHYYFS SRDRSSPGAL
NVYVKVNGGP QGNPVWNVSG VVTEGWVKAE LAISTFWPHF YQVIFESVSL KGHPGYIAVD
EVRVLAHPCR KAPHFLRLQN VEVNVGQNAT FQCIAGGKWS QHDKLWLQQW NGRDTALMVT
RVVNHRRFSA TVSVADTAQR SVSKYRCVIR SDGGSGVSNY AELIVKEPPT PIAPPELLAV
GATYLWIKPN ANSIIGDGPI ILKEVEYRTT TGTWAETHIV DSPNYKLWHL DPDVEYEIRV
LLTRPGEGGT GPPGPPLTTR TKCADPVHGP QNVEIVDIRA RQLTLQWEPF GYAVTRCHSY
NLTVQYQYVF NQQQYEAEEV IQTSSHYTLR GLRPFMTIRL RLLLSNPEGR MESEELVVQT
EEDVPGAVPL ESIQGGPFEE KIYIQWKPPN ETNGVITLYE INYKAVGSLD PSADLSSQRG
KVFKLRNETH HLFVGLYPGT TYSFTIKAST AKGFGPPVTT RIATKISAPS MPEYDTDTPL
NETDTTITVM LKPAQSRGAP VSVYQLVVKE ERLQKSRRAA DIIECFSVPV SYRNASSLDS
LHYFAAELKP ANLPVTQPFT VGDNKTYNGY WNPPLSPLKS YSIYFQALSK ANGETKINCV
RLATKGASTQ NSNTVEPEKQ VDNTVKMAGV IAGLLMFIII LLGVMLTIKR RKLAKKQKET
QSGAQREMGP VASADKPTTK LSASRNDEGF SSSSQDVNGF TDGSRGELSQ PTLTIQTHPY
RTCDPVEMSY PRDQFQPAIR VADLLQHITQ MKRGQGYGFK EEYEALPEGQ TASWDTAKED
ENRNKNRYGN IISYDHSRVR LLVLDGDPHS DYINANYIDG YHRPRHYIAT QGPMQETVKD
FWRMIWQENS ASIVMVTNLV EVGRHPAEHT VGNATLGRAA SPGMVKCVRY WPDDTEVYGD
IKVTLIETEP LAEYVIRTFT VQKKGYHEIR ELRLFHFTSW PDHGVPCYAT GLLGFVRQVK
FLNPPEAGPI VVHCSAGAGR TGCFIAIDTM LDMAENEGVV DIFNCVRELR AQRVNLVQTE
EQYVFVHDAI LEACLCGNTA IPVCEFRSLY YNISRLDPQT NSSQIKDEFQ TLNIVTPRVR
PEDCSIGLLP RNHDKNRSMD VLPLDRCLPF LISVDGESSN YINAALMDSH KQPAAFVVTQ
HPLPNTVADF WRLVFDYNCS SVVMLNEMDT AQFCMQYWPE KTSGCYGPIQ VEFVSADIDE
DIIHRIFRIC NMARPQDGYR IVQHLQYIGW PAYRDTPPSK RSLLKVVRRL EKWQEQYDGR
EGRTVVHCLN GGGRSGTFCA ICSVCEMIQQ QNIIDVFHIV KTLRNNKSNM VETLEQYKFV
YEVALEYLSS F*
mutated AA sequence MASLAALALS LLLRLQLPPL PGARAQSAPG GCSFDEHYSN CGYSVALGTN GFTWEQINTW
EKPMLDQAVP TGSFMMVNSS GRASGQKAHL LLPTLKENDT HCIDFHYYFS SRDRSSPGAL
NVYVKVNGGP QGNPVWNVSG VVTEGWVKAE LAISTFWPHF YQVIFESVSL KGHPGYIAVD
EVRVLAHPCR KAPHFLRLQN VEVNVGQNAT FQCIAGGKWS QHDKLWLQQW NGRDTALMVT
RVVNHRRFSA TVSVADTAQR SVSKYRCVIR SDGGSGVSNY AELIVKEPPT PIAPPELLAV
GATYLWIKPN ANSIIGDGPI ILKEVEYRTT TGTWAETHIV DSPNYKLWHL DPDVEYEIRV
LLTRPGEGGT GPPGPPLTTR TKCADPVHGP QNVEIVDIRA RQLTLQWEPF GYAVTRCHSY
NLTVQYQYVF NQQQYEAEEV IQTSSHYTLR GLRPFMTIRL RLLLSNPEGR MESEELVVQT
EEDVPGAVPL ESIQGGPFEE KIYIQWKPPN ETNGVITLYE INYKAVGSLD PSADLSSQRG
KVFKLRNETH HLFVGLYPGT TYSFTIKAST AKGFGPPVTT RIATKISAPS MPEYDTDTPL
NETDTTITVM LKPAQSRGAP VSVYQLVVKE ERLQKSRRAA DIIECFSVPV SYRNASSLDS
LHYFAAELKP ANLPVTQPFT VGDNKTYNGY WNPPLSPLKS YSIYFQALSK ANGETKINCV
RLATKGASTQ NSNTVEPEKQ VDNTVKMAGV IAGLLMFIII LLGVMLTIKR RKLAKKQKET
QSGAQREMGP VASADKPTTK LSASRNDEGF SSSSQDVNGF TDGSRGELSQ PTLTIQTHPY
RTCDPVEMSY PRDQFQPAIR VADLLQHITQ MKRGQGYGFK EEYEALPEGQ TASWDTAKED
ENRNKNRYGN IISYDHSRVR LLVLDGDPHS DYINANYIDG YHRPRHYIAT QGPMQETVKD
FWRMIWQENS ASIVMVTNLV EVGRHPAEHT VGNATLGRAA SPGMVKCVRY WPDDTEVYGD
IKVTLIETEP LAEYVIRTFT VQKKGYHEIR ELRLFHFTSW PDHGVPCYAT GLLGFVRQVK
FLNPPEAGPI VVHCSAGAGR TGCFIAIDTM LDMAENEGVV DIFNCVRELR AQRVNLVQTE
EQYVFVHDAI LEACLCGNTA IPVCEFRSLY YNISRLDPQT NSSQIKDEFQ TLNIVTPRVR
PEDCSIGLLP RNHDKNRSMD VLPLDRCLPF LISVDGESSN YINAALMDSH KQPAAFVVTQ
HPLPNTVADF WRLVFDYNCS SVVMLNEMDT AQFCMQYWPE KTSGCYGPIQ VEFVSADIDE
DIIHRIFRIC NMARPQDGYR IVQHLQYIGW PAYRDTPPSK RSLLKVVRRL EKWQEQYDGR
EGRTVVHCLN GGGRSGTFCA ICSVCEMIQQ QNIIDVFHIV KTLRNNKSNM VETLEQYKFV
YEVALEYLSS F*
speed 0.57 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table
Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.887415891759721 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr20:41818289C>GN/A show variant in all transcripts   IGV
HGNC symbol PTPRT
Ensembl transcript ID ENST00000373201
Genbank transcript ID N/A
UniProt peptide O14522
alteration type single base exchange
alteration region CDS
DNA changes c.85G>C
cDNA.322G>C
g.322G>C
AA changes A29P Score: 27 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 29
frameshift no
known variant Reference ID: rs2867655
databasehomozygous (G/G)heterozygousallele carriers
1000G14287052133
ExAC583107690
regulatory features H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
Non-Gene Associated, Regulatory Feature, Non-Gene associated regulatory feature
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)1.8861
1.8861
(flanking)0.1471
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost325sequence motif lost- wt: GCAG|gtga
 mu: CCAG.gtga
Donor marginally increased324wt: 0.9951 / mu: 0.9960 (marginal change - not scored)wt: GCCGCAGGTGAGTGC
mu: GCCCCAGGTGAGTGC		 CGCA|ggtg
Donor gained3200.47mu: GAGCGCCCCAGGTGA GCGC|ccca
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      29PPLPGARAQSAAGGCSFDEHYSNC
mutated  not conserved    29PPLPGARAQSAPGGCSFDEHYSN
Ptroglodytes  all identical  ENSPTRG00000013505  29PPLPGARAQSAAGGCSFDEHYSN
Mmulatta  no alignment  ENSMMUG00000001108  n/a
Fcatus  no alignment  ENSFCAG00000004770  n/a
Mmusculus  all identical  ENSMUSG00000053141  29PPLPGAGAQSAAGGCSFDEHYSN
Ggallus  no alignment  ENSGALG00000003488  n/a
Trubripes  no alignment  ENSTRUG00000008419  n/a
Drerio  no alignment  ENSDARG00000074781  n/a
Dmelanogaster  no alignment  FBgn0014007  n/a
Celegans  no alignment  F56D1.4  n/a
Xtropicalis  no alignment  ENSXETG00000012126  n/a
protein features
start (aa)end (aa)featuredetails 
26747TOPO_DOMExtracellular (Potential).lost
30191DOMAINMAM.might get lost (downstream of altered splice site)
6060CONFLICTW -> T (in Ref. 1; AAD09421).might get lost (downstream of altered splice site)
7878CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
9898CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
137137CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
193284DOMAINIg-like C2-type.might get lost (downstream of altered splice site)
208208CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
213213DISULFIDBy similarity.might get lost (downstream of altered splice site)
267267DISULFIDBy similarity.might get lost (downstream of altered splice site)
288379DOMAINFibronectin type-III 1.might get lost (downstream of altered splice site)
375375CONFLICTP -> A (in Ref. 1; AAD09421).might get lost (downstream of altered splice site)
386480DOMAINFibronectin type-III 2.might get lost (downstream of altered splice site)
421421CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
481584DOMAINFibronectin type-III 3.might get lost (downstream of altered splice site)
510510CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
547547CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
589726DOMAINFibronectin type-III 4.might get lost (downstream of altered splice site)
601601CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
654654CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
684684CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
748768TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
7691441TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
867867CONFLICTP -> L (in Ref. 1; AAD09421).might get lost (downstream of altered splice site)
871873HELIXmight get lost (downstream of altered splice site)
874882HELIXmight get lost (downstream of altered splice site)
889895HELIXmight get lost (downstream of altered splice site)
8891143DOMAINTyrosine-protein phosphatase 1.might get lost (downstream of altered splice site)
905908TURNmight get lost (downstream of altered splice site)
910915HELIXmight get lost (downstream of altered splice site)
925927HELIXmight get lost (downstream of altered splice site)
938941HELIXmight get lost (downstream of altered splice site)
944948STRANDmight get lost (downstream of altered splice site)
951953STRANDmight get lost (downstream of altered splice site)
957960STRANDmight get lost (downstream of altered splice site)
965967TURNmight get lost (downstream of altered splice site)
968978HELIXmight get lost (downstream of altered splice site)
982985STRANDmight get lost (downstream of altered splice site)
989991STRANDmight get lost (downstream of altered splice site)
10031009STRANDmight get lost (downstream of altered splice site)
10111020STRANDmight get lost (downstream of altered splice site)
10221033STRANDmight get lost (downstream of altered splice site)
10401047STRANDmight get lost (downstream of altered splice site)
10521052BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
10601072HELIXmight get lost (downstream of altered splice site)
10801083STRANDmight get lost (downstream of altered splice site)
10841084ACT_SITEPhosphocysteine intermediate (By similarity).might get lost (downstream of altered splice site)
10841090REGIONSubstrate binding (By similarity).might get lost (downstream of altered splice site)
10851088STRANDmight get lost (downstream of altered splice site)
10891107HELIXmight get lost (downstream of altered splice site)
11081110STRANDmight get lost (downstream of altered splice site)
11121122HELIXmight get lost (downstream of altered splice site)
11281128BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
11301145HELIXmight get lost (downstream of altered splice site)
11751437DOMAINTyrosine-protein phosphatase 2.might get lost (downstream of altered splice site)
13781378ACT_SITEPhosphocysteine intermediate (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 4296 / 4296
position (AA) of stopcodon in wt / mu AA sequence 1432 / 1432
position of stopcodon in wt / mu cDNA 4533 / 4533
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 238 / 238
chromosome 20
strand -1
last intron/exon boundary 4480
theoretical NMD boundary in CDS 4192
length of CDS 4296
coding sequence (CDS) position 85
cDNA position
(for ins/del: last normal base / first normal base)		 322
gDNA position
(for ins/del: last normal base / first normal base)		 322
chromosomal position
(for ins/del: last normal base / first normal base)		 41818289
original gDNA sequence snippet GCGCCCGGGCTCAGAGCGCCGCAGGTGAGTGCGCCCGCCCG
altered gDNA sequence snippet GCGCCCGGGCTCAGAGCGCCCCAGGTGAGTGCGCCCGCCCG
original cDNA sequence snippet GCGCCCGGGCTCAGAGCGCCGCAGGTGGCTGTTCCTTTGAT
altered cDNA sequence snippet GCGCCCGGGCTCAGAGCGCCCCAGGTGGCTGTTCCTTTGAT
wildtype AA sequence MASLAALALS LLLRLQLPPL PGARAQSAAG GCSFDEHYSN CGYSVALGTN GFTWEQINTW
EKPMLDQAVP TGSFMMVNSS GRASGQKAHL LLPTLKENDT HCIDFHYYFS SRDRSSPGAL
NVYVKVNGGP QGNPVWNVSG VVTEGWVKAE LAISTFWPHF YQVIFESVSL KGHPGYIAVD
EVRVLAHPCR KAPHFLRLQN VEVNVGQNAT FQCIAGGKWS QHDKLWLQQW NGRDTALMVT
RVVNHRRFSA TVSVADTAQR SVSKYRCVIR SDGGSGVSNY AELIVKEPPT PIAPPELLAV
GATYLWIKPN ANSIIGDGPI ILKEVEYRTT TGTWAETHIV DSPNYKLWHL DPDVEYEIRV
LLTRPGEGGT GPPGPPLTTR TKCADPVHGP QNVEIVDIRA RQLTLQWEPF GYAVTRCHSY
NLTVQYQYVF NQQQYEAEEV IQTSSHYTLR GLRPFMTIRL RLLLSNPEGR MESEELVVQT
EEDVPGAVPL ESIQGGPFEE KIYIQWKPPN ETNGVITLYE INYKAVGSLD PSADLSSQRG
KVFKLRNETH HLFVGLYPGT TYSFTIKAST AKGFGPPVTT RIATKISAPS MPEYDTDTPL
NETDTTITVM LKPAQSRGAP VSVYQLVVKE ERLQKSRRAA DIIECFSVPV SYRNASSLDS
LHYFAAELKP ANLPVTQPFT VGDNKTYNGY WNPPLSPLKS YSIYFQALSK ANGETKINCV
RLATKGASTQ NSNTVEPEKQ VDNTVKMAGV IAGLLMFIII LLGVMLTIKR RKLAKKQKET
QSGAQREMGP VASADKPTTK LSASRNDEGF SSSSQDVNGF TDGSRGELSQ PTLTIQTHPY
RTCDPVEMSY PRDQFQPAIR VADLLQHITQ MKRGQGYGFK EEYEALPEGQ TASWDTAKED
ENRNKNRYGN IISYDHSRVR LLVLDGDPHS DYINANYIDG YHRPRHYIAT QGPMQETVKD
FWRMIWQENS ASIVMVTNLV EVGRVKCVRY WPDDTEVYGD IKVTLIETEP LAEYVIRTFT
VQKKGYHEIR ELRLFHFTSW PDHGVPCYAT GLLGFVRQVK FLNPPEAGPI VVHCSAGAGR
TGCFIAIDTM LDMAENEGVV DIFNCVRELR AQRVNLVQTE EQYVFVHDAI LEACLCGNTA
IPVCEFRSLY YNISRLDPQT NSSQIKDEFQ TLNIVTPRVR PEDCSIGLLP RNHDKNRSMD
VLPLDRCLPF LISVDGESSN YINAALMDSH KQPAAFVVTQ HPLPNTVADF WRLVFDYNCS
SVVMLNEMDT AQFCMQYWPE KTSGCYGPIQ VEFVSADIDE DIIHRIFRIC NMARPQDGYR
IVQHLQYIGW PAYRDTPPSK RSLLKVVRRL EKWQEQYDGR EGRTVVHCLN GGGRSGTFCA
ICSVCEMIQQ QNIIDVFHIV KTLRNNKSNM VETLEQYKFV YEVALEYLSS F*
mutated AA sequence MASLAALALS LLLRLQLPPL PGARAQSAPG GCSFDEHYSN CGYSVALGTN GFTWEQINTW
EKPMLDQAVP TGSFMMVNSS GRASGQKAHL LLPTLKENDT HCIDFHYYFS SRDRSSPGAL
NVYVKVNGGP QGNPVWNVSG VVTEGWVKAE LAISTFWPHF YQVIFESVSL KGHPGYIAVD
EVRVLAHPCR KAPHFLRLQN VEVNVGQNAT FQCIAGGKWS QHDKLWLQQW NGRDTALMVT
RVVNHRRFSA TVSVADTAQR SVSKYRCVIR SDGGSGVSNY AELIVKEPPT PIAPPELLAV
GATYLWIKPN ANSIIGDGPI ILKEVEYRTT TGTWAETHIV DSPNYKLWHL DPDVEYEIRV
LLTRPGEGGT GPPGPPLTTR TKCADPVHGP QNVEIVDIRA RQLTLQWEPF GYAVTRCHSY
NLTVQYQYVF NQQQYEAEEV IQTSSHYTLR GLRPFMTIRL RLLLSNPEGR MESEELVVQT
EEDVPGAVPL ESIQGGPFEE KIYIQWKPPN ETNGVITLYE INYKAVGSLD PSADLSSQRG
KVFKLRNETH HLFVGLYPGT TYSFTIKAST AKGFGPPVTT RIATKISAPS MPEYDTDTPL
NETDTTITVM LKPAQSRGAP VSVYQLVVKE ERLQKSRRAA DIIECFSVPV SYRNASSLDS
LHYFAAELKP ANLPVTQPFT VGDNKTYNGY WNPPLSPLKS YSIYFQALSK ANGETKINCV
RLATKGASTQ NSNTVEPEKQ VDNTVKMAGV IAGLLMFIII LLGVMLTIKR RKLAKKQKET
QSGAQREMGP VASADKPTTK LSASRNDEGF SSSSQDVNGF TDGSRGELSQ PTLTIQTHPY
RTCDPVEMSY PRDQFQPAIR VADLLQHITQ MKRGQGYGFK EEYEALPEGQ TASWDTAKED
ENRNKNRYGN IISYDHSRVR LLVLDGDPHS DYINANYIDG YHRPRHYIAT QGPMQETVKD
FWRMIWQENS ASIVMVTNLV EVGRVKCVRY WPDDTEVYGD IKVTLIETEP LAEYVIRTFT
VQKKGYHEIR ELRLFHFTSW PDHGVPCYAT GLLGFVRQVK FLNPPEAGPI VVHCSAGAGR
TGCFIAIDTM LDMAENEGVV DIFNCVRELR AQRVNLVQTE EQYVFVHDAI LEACLCGNTA
IPVCEFRSLY YNISRLDPQT NSSQIKDEFQ TLNIVTPRVR PEDCSIGLLP RNHDKNRSMD
VLPLDRCLPF LISVDGESSN YINAALMDSH KQPAAFVVTQ HPLPNTVADF WRLVFDYNCS
SVVMLNEMDT AQFCMQYWPE KTSGCYGPIQ VEFVSADIDE DIIHRIFRIC NMARPQDGYR
IVQHLQYIGW PAYRDTPPSK RSLLKVVRRL EKWQEQYDGR EGRTVVHCLN GGGRSGTFCA
ICSVCEMIQQ QNIIDVFHIV KTLRNNKSNM VETLEQYKFV YEVALEYLSS F*
speed 0.92 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project
back to results table

Problems