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 4 transcript(s)...
Querying Taster for transcript #1: ENST00000356692
Querying Taster for transcript #2: ENST00000394284
Querying Taster for transcript #3: ENST00000295862
Querying Taster for transcript #4: ENST00000533473
MT speed 0 s - this script 3.414455 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
EBLN2polymorphism_automatic8.98947583038989e-13simple_aaeS46Psingle base exchangers2231924show file
PPP4R2polymorphism_automatic1.46040679993575e-07without_aaesingle base exchangers2231924show file
PPP4R2polymorphism_automatic1.46040679993575e-07without_aaesingle base exchangers2231924show file
PPP4R2polymorphism_automatic1.46040679993575e-07without_aaesingle base exchangers2231924show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.999999999999101 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:73111368T>CN/A show variant in all transcripts   IGV
HGNC symbol EBLN2
Ensembl transcript ID ENST00000533473
Genbank transcript ID NM_018029
UniProt peptide Q6P2I7
alteration type single base exchange
alteration region CDS
DNA changes c.136T>C
cDNA.559T>C
g.559T>C
AA changes S46P Score: 74 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 46
frameshift no
known variant Reference ID: rs2231924
databasehomozygous (C/C)heterozygousallele carriers
1000G71312111924
ExAC13631550519136
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-2.430.001
-0.9990.004
(flanking)0.5740.028
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 559
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      46NKIKELSRNQFSTMSHLRKDSQPS
mutated  not conserved    46NKIKELSRNQFPTMSHLRKDSQP
Ptroglodytes  no homologue    
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  no homologue    
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features no protein features affected
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 819 / 819
position (AA) of stopcodon in wt / mu AA sequence 273 / 273
position of stopcodon in wt / mu cDNA 1242 / 1242
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 424 / 424
chromosome 3
strand 1
last intron/exon boundary 1
theoretical NMD boundary in CDS cannot be calculated, too little distance between start ATG and last intron/exon boundary
length of CDS 819
coding sequence (CDS) position 136
cDNA position
(for ins/del: last normal base / first normal base)		 559
gDNA position
(for ins/del: last normal base / first normal base)		 559
chromosomal position
(for ins/del: last normal base / first normal base)		 73111368
original gDNA sequence snippet AATTAAGTCGGAACCAATTTTCCACAATGTCTCATCTAAGA
altered gDNA sequence snippet AATTAAGTCGGAACCAATTTCCCACAATGTCTCATCTAAGA
original cDNA sequence snippet AATTAAGTCGGAACCAATTTTCCACAATGTCTCATCTAAGA
altered cDNA sequence snippet AATTAAGTCGGAACCAATTTCCCACAATGTCTCATCTAAGA
wildtype AA sequence MGYFLKLYAY VNSHSLFVWV CDRSYKRSFR PMILNKIKEL SRNQFSTMSH LRKDSQPSSP
GDDAMDRSGL PDLQGRFELS GKNRQYPLDA LEPQPSIGDI KDIKKAAKSM LDPAHKSHFH
PVTPSLVFLC FIFDGLHQAL LSVGVSKRSN TVVGNENEER GTPYASRFKD MPNFIALEKS
SVLRHCCDLL IGIAAGSSDK ICTSSLQVQR RFKAMMASIG RLSHGESADL LISCNAESAI
GWISSRPWVG ELMFTLLFGD FESPLHKLRK SS*
mutated AA sequence MGYFLKLYAY VNSHSLFVWV CDRSYKRSFR PMILNKIKEL SRNQFPTMSH LRKDSQPSSP
GDDAMDRSGL PDLQGRFELS GKNRQYPLDA LEPQPSIGDI KDIKKAAKSM LDPAHKSHFH
PVTPSLVFLC FIFDGLHQAL LSVGVSKRSN TVVGNENEER GTPYASRFKD MPNFIALEKS
SVLRHCCDLL IGIAAGSSDK ICTSSLQVQR RFKAMMASIG RLSHGESADL LISCNAESAI
GWISSRPWVG ELMFTLLFGD FESPLHKLRK SS*
speed 0.86 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: without_aae, prob: 0.99999985395932 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:73111368T>CN/A show variant in all transcripts   IGV
HGNC symbol PPP4R2
Ensembl transcript ID ENST00000394284
Genbank transcript ID N/A
UniProt peptide N/A
alteration type single base exchange
alteration region intron
DNA changes g.65433T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs2231924
databasehomozygous (C/C)heterozygousallele carriers
1000G71312111924
ExAC13631550519136
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-2.430.001
-0.9990.004
(flanking)0.5740.028
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 1157
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features N/A
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 199 / 199
chromosome 3
strand 1
last intron/exon boundary 956
theoretical NMD boundary in CDS 707
length of CDS 1083
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 65433
chromosomal position
(for ins/del: last normal base / first normal base)		 73111368
original gDNA sequence snippet AATTAAGTCGGAACCAATTTTCCACAATGTCTCATCTAAGA
altered gDNA sequence snippet AATTAAGTCGGAACCAATTTCCCACAATGTCTCATCTAAGA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MDVERLQEAL KDFEKRGKKE VCPVLDQFLC HVAKTGETII PFTIQRLCEL LTDPRRNYTG
TDKFLRGVEK NVMVVSCVYP SSEKNNSNSL NRMNGVMFPG NSPSYTERSN INGPGTPRPL
NRPKVSLSAP MTTNGLPEST DSKEANLQQN EEKNHSDSST SESEVSSVSP LKNKHPDEDA
VEAEGHEVKR LRFDKEGEVR ETASQTTSSE ISSVMVGETE ASSSSQDKDK DSRCTRQHCT
EEDEEEDEEE EEESFMTSRE MIPERKNQEK ESDDALTVNE ETSEENNQME ESDVSQAEKD
LLHSEGSENE GPVSSSSSDC RETEELVGSN SSKTGEILSE SSMENDDEAT EVTDEPMEQD
*
mutated AA sequence N/A
speed 0.26 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: without_aae, prob: 0.99999985395932 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:73111368T>CN/A show variant in all transcripts   IGV
HGNC symbol PPP4R2
Ensembl transcript ID ENST00000295862
Genbank transcript ID N/A
UniProt peptide N/A
alteration type single base exchange
alteration region intron
DNA changes g.65433T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs2231924
databasehomozygous (C/C)heterozygousallele carriers
1000G71312111924
ExAC13631550519136
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-2.430.001
-0.9990.004
(flanking)0.5740.028
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 1157
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features N/A
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 367 / 367
chromosome 3
strand 1
last intron/exon boundary 1127
theoretical NMD boundary in CDS 710
length of CDS 1086
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 65433
chromosomal position
(for ins/del: last normal base / first normal base)		 73111368
original gDNA sequence snippet AATTAAGTCGGAACCAATTTTCCACAATGTCTCATCTAAGA
altered gDNA sequence snippet AATTAAGTCGGAACCAATTTCCCACAATGTCTCATCTAAGA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MDDFRTSAPE PRGPPNPNVE YIPFDEMKER ILKIVTGFNG IPFTIQRLCE LLTDPRRNYT
GTDKFLRGVE KNVMVVSCVY PSSEKNNSNS LNRMNGVMFP GNSPSYTERS NINGPGTPRP
LNRPKVSLSA PMTTNGLPES TDSKEANLQQ NEEKNHSDSS TSESEVSSVS PLKNKHPDED
AVEAEGHEVK RLRFDKEGEV RETASQTTSS EISSVMVGET EASSSSQDKD KDSRCTRQHC
TEEDEEEDEE EEEESFMTSR EMIPERKNQE KESDDALTVN EETSEENNQM EESDVSQAEK
DLLHSEGSEN EGPVSSSSSD CRETEELVGS NSSKTGEILS ESSMENDDEA TEVTDEPMEQ
D*
mutated AA sequence N/A
speed 0.24 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: without_aae, prob: 0.99999985395932 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • homozygous in TGP or ExAC
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:73111368T>CN/A show variant in all transcripts   IGV
HGNC symbol PPP4R2
Ensembl transcript ID ENST00000356692
Genbank transcript ID NM_174907
UniProt peptide N/A
alteration type single base exchange
alteration region intron
DNA changes g.65433T>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs2231924
databasehomozygous (C/C)heterozygousallele carriers
1000G71312111924
ExAC13631550519136
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-2.430.001
-0.9990.004
(flanking)0.5740.028
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 1157
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features N/A
length of protein N/A
AA sequence altered N/A
position of stopcodon in wt / mu CDS N/A
position (AA) of stopcodon in wt / mu AA sequence N/A
position of stopcodon in wt / mu cDNA N/A
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 254 / 254
chromosome 3
strand 1
last intron/exon boundary 1182
theoretical NMD boundary in CDS 878
length of CDS 1254
coding sequence (CDS) position N/A
cDNA position
(for ins/del: last normal base / first normal base)		 N/A
gDNA position
(for ins/del: last normal base / first normal base)		 65433
chromosomal position
(for ins/del: last normal base / first normal base)		 73111368
original gDNA sequence snippet AATTAAGTCGGAACCAATTTTCCACAATGTCTCATCTAAGA
altered gDNA sequence snippet AATTAAGTCGGAACCAATTTCCCACAATGTCTCATCTAAGA
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MDVERLQEAL KDFEKRGKKE VCPVLDQFLC HVAKTGETMI QWSQFKGYFI FKLEKVMDDF
RTSAPEPRGP PNPNVEYIPF DEMKERILKI VTGFNGIPFT IQRLCELLTD PRRNYTGTDK
FLRGVEKNVM VVSCVYPSSE KNNSNSLNRM NGVMFPGNSP SYTERSNING PGTPRPLNRP
KVSLSAPMTT NGLPESTDSK EANLQQNEEK NHSDSSTSES EVSSVSPLKN KHPDEDAVEA
EGHEVKRLRF DKEGEVRETA SQTTSSEISS VMVGETEASS SSQDKDKDSR CTRQHCTEED
EEEDEEEEEE SFMTSREMIP ERKNQEKESD DALTVNEETS EENNQMEESD VSQAEKDLLH
SEGSENEGPV SSSSSDCRET EELVGSNSSK TGEILSESSM ENDDEATEVT DEPMEQD*
mutated AA sequence N/A
speed 0.28 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

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