Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 0.904047569504736 (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) chr1:29631909A>GN/A show variant in all transcripts   IGV
HGNC symbol PTPRU
Ensembl transcript ID ENST00000373779
Genbank transcript ID NM_133178
UniProt peptide Q92729
alteration type single base exchange
alteration region CDS
DNA changes c.2789A>G
cDNA.2918A>G
g.68882A>G
AA changes N930S Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 930
frameshift no
known variant Reference ID: rs2235937
databasehomozygous (G/G)heterozygousallele carriers
1000G29111031394
ExAC57342129927033
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.4590.905
0.340.888
(flanking)0.0270.886
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained688810.82mu: ACCCCAGTGCCGACT CCCA|gtgc
Donor gained688760.88mu: GGGAGACCCCAGTGC GAGA|cccc
distance from splice site 32
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      930RVKLHPMLGDPNADYINANYIDGY
mutated  all conserved    930RVKLHPMLGDPSADYINANYIDG
Ptroglodytes  all identical  ENSPTRG00000000447  905LGDPNADYINANYIDIRINREG
Mmulatta  all identical  ENSMMUG00000015661  927RVKLHPMLGDPNADYINANYIDG
Fcatus  no homologue    
Mmusculus  all conserved  ENSMUSG00000028909  940HVKLHPMLADPDADYISANYIDG
Ggallus  all identical  ENSGALG00000001443  929RVKLHPLLGDPNSDYINANYIDG
Trubripes  all identical  ENSTRUG00000014224  872RVKLHPLLGDPNSDYINANYIDG
Drerio  no homologue    
Dmelanogaster  not conserved  FBgn0014007  939RVKLAVINGLQTTDYINA
Celegans  not conserved  F56D1.4  874RVKLKKINGDDYSDYINANFIK
Xtropicalis  all conserved  ENSXETG00000005931  930RVRLHPLQAECSSEEINANYIDG
protein features
start (aa)end (aa)featuredetails 
7711446TOPO_DOMCytoplasmic (Potential).lost
8881144DOMAINTyrosine-protein phosphatase 1.lost
10531053BINDINGSubstrate (Potential).might get lost (downstream of altered splice site)
10851085MUTAGENC->S: Loss of phosphatase activity toward CTNNB1. Loss of the inhibitory effect on CTNNB1 transcriptional activity without effect on interaction with CTNNB1; when associated with S-1380.might get lost (downstream of altered splice site)
10851085ACT_SITEPhosphocysteine intermediate (By similarity).might get lost (downstream of altered splice site)
10851091REGIONSubstrate binding (By similarity).might get lost (downstream of altered splice site)
11291129BINDINGSubstrate (By similarity).might get lost (downstream of altered splice site)
11761439DOMAINTyrosine-protein phosphatase 2.might get lost (downstream of altered splice site)
12151215CONFLICTP -> A (in Ref. 5; AAB07074).might get lost (downstream of altered splice site)
12451245CONFLICTA -> R (in Ref. 4; AAC51938).might get lost (downstream of altered splice site)
13801380MUTAGENC->S: No effect on phosphatase activity toward CTNNB1. Loss of the inhibitory effect on CTNNB1 transcriptional activity without effect on interaction with CTNNB1; when associated with S-1085.might get lost (downstream of altered splice site)
13801380ACT_SITEPhosphocysteine intermediate (By similarity).might get lost (downstream of altered splice site)
13991399CONFLICTM -> I (in Ref. 4; AAC51938).might get lost (downstream of altered splice site)
14361436CONFLICTA -> V (in Ref. 5; AAB07074).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 4311 / 4311
position (AA) of stopcodon in wt / mu AA sequence 1437 / 1437
position of stopcodon in wt / mu cDNA 4440 / 4440
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 130 / 130
chromosome 1
strand 1
last intron/exon boundary 4378
theoretical NMD boundary in CDS 4198
length of CDS 4311
coding sequence (CDS) position 2789
cDNA position
(for ins/del: last normal base / first normal base)		 2918
gDNA position
(for ins/del: last normal base / first normal base)		 68882
chromosomal position
(for ins/del: last normal base / first normal base)		 29631909
original gDNA sequence snippet CCCGATGCTGGGAGACCCCAATGCCGACTACATTAATGCCA
altered gDNA sequence snippet CCCGATGCTGGGAGACCCCAGTGCCGACTACATTAATGCCA
original cDNA sequence snippet CCCGATGCTGGGAGACCCCAATGCCGACTACATTAATGCCA
altered cDNA sequence snippet CCCGATGCTGGGAGACCCCAGTGCCGACTACATTAATGCCA
wildtype AA sequence MARAQALVLA LTFQLCAPET ETPAAGCTFE EASDPAVPCE YSQAQYDDFQ WEQVRIHPGT
RAPADLPHGS YLMVNTSQHA PGQRAHVIFQ SLSENDTHCV QFSYFLYSRD GHSPGTLGVY
VRVNGGPLGS AVWNMTGSHG RQWHQAELAV STFWPNEYQV LFEALISPDR RGYMGLDDIL
LLSYPCAKAP HFSRLGDVEV NAGQNASFQC MAAGRAAEAE RFLLQRQSGA LVPAAGVRHI
SHRRFLATFP LAAVSRAEQD LYRCVSQAPR GAGVSNFAEL IVKEPPTPIA PPQLLRAGPT
YLIIQLNTNS IIGDGPIVRK EIEYRMARGP WAEVHAVSLQ TYKLWHLDPD TEYEISVLLT
RPGDGGTGRP GPPLISRTKC AEPMRAPKGL AFAEIQARQL TLQWEPLGYN VTRCHTYTVS
LCYHYTLGSS HNQTIRECVK TEQGVSRYTI KNLLPYRNVH VRLVLTNPEG RKEGKEVTFQ
TDEDVPSGIA AESLTFTPLE DMIFLKWEEP QEPNGLITQY EISYQSIESS DPAVNVPGPR
RTISKLRNET YHVFSNLHPG TTYLFSVRAR TGKGFGQAAL TEITTNISAP SFDYADMPSP
LGESENTITV LLRPAQGRGA PISVYQVIVE EERARRLRRE PGGQDCFPVP LTFEAALARG
LVHYFGAELA ASSLPEAMPF TVGDNQTYRG FWNPPLEPRK AYLIYFQAAS HLKGETRLNC
IRIARKAACK ESKRPLEVSQ RSEEMGLILG ICAGGLAVLI LLLGAIIVII RKGKPVNMTK
ATVNYRQEKT HMMSAVDRSF TDQSTLQEDE RLGLSFMDTH GYSTRGDQRS GGVTEASSLL
GGSPRRPCGR KGSPYHTGQL HPAVRVADLL QHINQMKTAE GYGFKQEYES FFEGWDATKK
KDKVKGSRQE PMPAYDRHRV KLHPMLGDPN ADYINANYID GYHRSNHFIA TQGPKPEMVY
DFWRMVWQEH CSSIVMITKL VEVGRVKCSR YWPEDSDTYG DIKIMLVKTE TLAEYVVRTF
ALERRGYSAR HEVRQFHFTA WPEHGVPYHA TGLLAFIRRV KASTPPDAGP IVIHCSAGTG
RTGCYIVLDV MLDMAECEGV VDIYNCVKTL CSRRVNMIQT EEQYIFIHDA ILEACLCGET
TIPVSEFKAT YKEMIRIDPQ SNSSQLREEF QTLNSVTPPL DVEECSIALL PRNRDKNRSM
DVLPPDRCLP FLISTDGDSN NYINAALTDS YTRSAAFIVT LHPLQSTTPD FWRLVYDYGC
TSIVMLNQLN QSNSAWPCLQ YWPEPGRQQY GLMEVEFMSG TADEDLVARV FRVQNISRLQ
EGHLLVRHFQ FLRWSAYRDT PDSKKAFLHL LAEVDKWQAE SGDGRTIVHC LNGGGRSGTF
CACATVLEMI RCHNLVDVFF AAKTLRNYKP NMVETMDQYH FCYDVALEYL EGLESR*
mutated AA sequence MARAQALVLA LTFQLCAPET ETPAAGCTFE EASDPAVPCE YSQAQYDDFQ WEQVRIHPGT
RAPADLPHGS YLMVNTSQHA PGQRAHVIFQ SLSENDTHCV QFSYFLYSRD GHSPGTLGVY
VRVNGGPLGS AVWNMTGSHG RQWHQAELAV STFWPNEYQV LFEALISPDR RGYMGLDDIL
LLSYPCAKAP HFSRLGDVEV NAGQNASFQC MAAGRAAEAE RFLLQRQSGA LVPAAGVRHI
SHRRFLATFP LAAVSRAEQD LYRCVSQAPR GAGVSNFAEL IVKEPPTPIA PPQLLRAGPT
YLIIQLNTNS IIGDGPIVRK EIEYRMARGP WAEVHAVSLQ TYKLWHLDPD TEYEISVLLT
RPGDGGTGRP GPPLISRTKC AEPMRAPKGL AFAEIQARQL TLQWEPLGYN VTRCHTYTVS
LCYHYTLGSS HNQTIRECVK TEQGVSRYTI KNLLPYRNVH VRLVLTNPEG RKEGKEVTFQ
TDEDVPSGIA AESLTFTPLE DMIFLKWEEP QEPNGLITQY EISYQSIESS DPAVNVPGPR
RTISKLRNET YHVFSNLHPG TTYLFSVRAR TGKGFGQAAL TEITTNISAP SFDYADMPSP
LGESENTITV LLRPAQGRGA PISVYQVIVE EERARRLRRE PGGQDCFPVP LTFEAALARG
LVHYFGAELA ASSLPEAMPF TVGDNQTYRG FWNPPLEPRK AYLIYFQAAS HLKGETRLNC
IRIARKAACK ESKRPLEVSQ RSEEMGLILG ICAGGLAVLI LLLGAIIVII RKGKPVNMTK
ATVNYRQEKT HMMSAVDRSF TDQSTLQEDE RLGLSFMDTH GYSTRGDQRS GGVTEASSLL
GGSPRRPCGR KGSPYHTGQL HPAVRVADLL QHINQMKTAE GYGFKQEYES FFEGWDATKK
KDKVKGSRQE PMPAYDRHRV KLHPMLGDPS ADYINANYID GYHRSNHFIA TQGPKPEMVY
DFWRMVWQEH CSSIVMITKL VEVGRVKCSR YWPEDSDTYG DIKIMLVKTE TLAEYVVRTF
ALERRGYSAR HEVRQFHFTA WPEHGVPYHA TGLLAFIRRV KASTPPDAGP IVIHCSAGTG
RTGCYIVLDV MLDMAECEGV VDIYNCVKTL CSRRVNMIQT EEQYIFIHDA ILEACLCGET
TIPVSEFKAT YKEMIRIDPQ SNSSQLREEF QTLNSVTPPL DVEECSIALL PRNRDKNRSM
DVLPPDRCLP FLISTDGDSN NYINAALTDS YTRSAAFIVT LHPLQSTTPD FWRLVYDYGC
TSIVMLNQLN QSNSAWPCLQ YWPEPGRQQY GLMEVEFMSG TADEDLVARV FRVQNISRLQ
EGHLLVRHFQ FLRWSAYRDT PDSKKAFLHL LAEVDKWQAE SGDGRTIVHC LNGGGRSGTF
CACATVLEMI RCHNLVDVFF AAKTLRNYKP NMVETMDQYH FCYDVALEYL EGLESR*
speed 0.56 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