Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 8.88930669819938e-07 (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) chr10:55955444T>GN/A show variant in all transcripts   IGV
HGNC symbol PCDH15
Ensembl transcript ID ENST00000409834
Genbank transcript ID N/A
UniProt peptide Q96QU1
alteration type single base exchange
alteration region CDS
DNA changes c.116A>C
cDNA.692A>C
g.1432259A>C
AA changes D39A Score: 126 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 39
frameshift no
known variant Reference ID: rs4935502
databasehomozygous (G/G)heterozygousallele carriers
1000G4817671248
ExAC56151764923264
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)2.2451
4.7741
(flanking)5.7841
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 lost1432260sequence motif lost- wt: AGAT|gtaa
 mu: AGCT.gtaa
Donor marginally increased1432252wt: 0.9798 / mu: 0.9914 (marginal change - not scored)wt: AGGACATAGAAGATG
mu: AGGACATAGAAGCTG		 GACA|taga
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      39LRIVALDKDIEDVPPSGVPTKDPE
mutated  not conserved    39LRIVALDKDIEAVPPSGVPTKDP
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000009794  435LRIVALDKDIED-------TKDP
Fcatus  no alignment  ENSFCAG00000010122  n/a
Mmusculus  all identical  ENSMUSG00000052613  440LRIVALDKDIED-------TKDP
Ggallus  all conserved  ENSGALG00000002744  383LQITVLDNDVEE-------TKDP
Trubripes  all conserved  ENSTRUG00000010819  424LEIIALDNDIEE-------TKDP
Drerio  all conserved  ENSDARG00000008127  383LAIIVLDNDIEE-------TKDP
Dmelanogaster  all identical  FBgn0039709  427ISFMTTDADLSD--------SDP
Celegans  all identical  F15B9.7  399AVIATVKATDEDFGTNG------
Xtropicalis  all conserved  ENSXETG00000018945  386LKFVALDNDIEE-------TKDP
protein features
start (aa)end (aa)featuredetails 
271376TOPO_DOMExtracellular (Potential).lost
40147DOMAINCadherin 1.might get lost (downstream of altered splice site)
5252CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
9797CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
148265DOMAINCadherin 2.might get lost (downstream of altered splice site)
201201CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
261261CONFLICTL -> S (in Ref. 1; AAK31581).might get lost (downstream of altered splice site)
278395DOMAINCadherin 3.might get lost (downstream of altered splice site)
396509DOMAINCadherin 4.might get lost (downstream of altered splice site)
419419CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
467467CONFLICTQ -> L (in Ref. 1; AAK31581).might get lost (downstream of altered splice site)
510616DOMAINCadherin 5.might get lost (downstream of altered splice site)
559559CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
617717DOMAINCadherin 6.might get lost (downstream of altered splice site)
662662CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
719819DOMAINCadherin 7.might get lost (downstream of altered splice site)
724724CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
768768CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
820926DOMAINCadherin 8.might get lost (downstream of altered splice site)
821821CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
851851CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
9271035DOMAINCadherin 9.might get lost (downstream of altered splice site)
10371144DOMAINCadherin 10.might get lost (downstream of altered splice site)
10641064CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
10841084CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
11451259DOMAINCadherin 11.might get lost (downstream of altered splice site)
11751175CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
12761276CONFLICTQ -> R (in Ref. 1; AAK31581).might get lost (downstream of altered splice site)
13771397TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
13981955TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
14351443COMPBIASPoly-Pro.might get lost (downstream of altered splice site)
17461752COMPBIASPoly-Pro.might get lost (downstream of altered splice site)
18151823COMPBIASPoly-Pro.might get lost (downstream of altered splice site)
18261831COMPBIASPoly-Pro.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3453 / 3453
position (AA) of stopcodon in wt / mu AA sequence 1151 / 1151
position of stopcodon in wt / mu cDNA 4029 / 4029
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 577 / 577
chromosome 10
strand -1
last intron/exon boundary 3963
theoretical NMD boundary in CDS 3336
length of CDS 3453
coding sequence (CDS) position 116
cDNA position
(for ins/del: last normal base / first normal base)		 692
gDNA position
(for ins/del: last normal base / first normal base)		 1432259
chromosomal position
(for ins/del: last normal base / first normal base)		 55955444
original gDNA sequence snippet TCTGGACAAGGACATAGAAGATGTAAGTTAAATACATATTT
altered gDNA sequence snippet TCTGGACAAGGACATAGAAGCTGTAAGTTAAATACATATTT
original cDNA sequence snippet TCTGGACAAGGACATAGAAGATGTTCCACCCAGTGGAGTTC
altered cDNA sequence snippet TCTGGACAAGGACATAGAAGCTGTTCCACCCAGTGGAGTTC
wildtype AA sequence MPSYQGYILE SAPVGATISD SLNLTSPLRI VALDKDIEDV PPSGVPTKDP ELHLFLNDYT
SVFTVTQTGI TRYLTLLQPV DREEQQTYTF SITAFDGVQE SEPVIVNIQV MDANDNTPTF
PEISYDVYVY TDMRPGDSVI QLTAVDADEG SNGEITYEIL VGAQGDFIIN KTTGLITIAP
GVEMIVGRTY ALTVQAADNA PPAERRNSIC TVYIEVLPPN NQSPPRFPQL MYSLEISEAM
RVGAVLLNLQ ATDREGDSIT YAIENGDPQR VFNLSETTGI LTLGKALDRE STDRYILIIT
ASDGRPDGTS TATVNIVVTD VNDNAPVFDP YLPRNLSVVE EEANAFVGQV KATDPDAGIN
GQVHYSLGNF NNLFRITSNG SIYTAVKLNR EVRDYYELVV VATDGAVHPR HSTLTLAIKV
LDIDDNSPVF TNSTYTVLVE ENLPAGTTIL QIEAKDVDLG ANVSYRIRSP EVKHFFALHP
FTGELSLLRS LDYEAFPDQE ASITFLVEAF DIYGTMPPGI ATVTVIVKDM NDYPPVFSKR
IYKGMVAPDA VKGTPITTVY AEDADPPGLP ASRVRYRVDD VQFPYPASIF EVEEDSGRVI
TRVNLNEEPT TIFKLVVVAF DDGEPVMSSS ATVKILVLHP GEIPRFTQEE YRPPPVSELA
TKGTMVGVIS AAAINQSIVY SIVSGNEEDT FGINNITGVI YVNGPLDYET RTSYVLRVQA
DSLEVVLANL RVPSKSNTAK VYIEIQDENN HPPVFQKKFY IGGVSEDARM FTSVLRVKAT
DKDTGNYSVM AYRLIIPPIK EGKEGFVVET YTGLIKTAML FHNMRRSYFK FQVIATDDYG
KGLSGKADVL VSVVNQLDMQ VIVSNVPPTL VEKKIEDLTE ILDRYVQEQI PGAKVVVESI
GARRHGDAFS LEDYTKCDLT VYAIDPQTNR AIDRNELFKF LDGKLLDINK DFQPYYGEGG
RILEIRTPEA VTSIKKRGES LGYTEGALLA LAFIIILCCI PAILVVLVSY RQFKVRQAEC
TKTARIQAAL PAAKPAVPAP APVAAPPPPP PPPPGAHLYE ELGDSSMHKN YPWSLELILA
RNMDKIITVM SMGMKCLNMG VAVDCYHQLD RRNMVRWLVK LRKNMRRKRK SQRKLKNQRL
KLESLVRRKK *
mutated AA sequence MPSYQGYILE SAPVGATISD SLNLTSPLRI VALDKDIEAV PPSGVPTKDP ELHLFLNDYT
SVFTVTQTGI TRYLTLLQPV DREEQQTYTF SITAFDGVQE SEPVIVNIQV MDANDNTPTF
PEISYDVYVY TDMRPGDSVI QLTAVDADEG SNGEITYEIL VGAQGDFIIN KTTGLITIAP
GVEMIVGRTY ALTVQAADNA PPAERRNSIC TVYIEVLPPN NQSPPRFPQL MYSLEISEAM
RVGAVLLNLQ ATDREGDSIT YAIENGDPQR VFNLSETTGI LTLGKALDRE STDRYILIIT
ASDGRPDGTS TATVNIVVTD VNDNAPVFDP YLPRNLSVVE EEANAFVGQV KATDPDAGIN
GQVHYSLGNF NNLFRITSNG SIYTAVKLNR EVRDYYELVV VATDGAVHPR HSTLTLAIKV
LDIDDNSPVF TNSTYTVLVE ENLPAGTTIL QIEAKDVDLG ANVSYRIRSP EVKHFFALHP
FTGELSLLRS LDYEAFPDQE ASITFLVEAF DIYGTMPPGI ATVTVIVKDM NDYPPVFSKR
IYKGMVAPDA VKGTPITTVY AEDADPPGLP ASRVRYRVDD VQFPYPASIF EVEEDSGRVI
TRVNLNEEPT TIFKLVVVAF DDGEPVMSSS ATVKILVLHP GEIPRFTQEE YRPPPVSELA
TKGTMVGVIS AAAINQSIVY SIVSGNEEDT FGINNITGVI YVNGPLDYET RTSYVLRVQA
DSLEVVLANL RVPSKSNTAK VYIEIQDENN HPPVFQKKFY IGGVSEDARM FTSVLRVKAT
DKDTGNYSVM AYRLIIPPIK EGKEGFVVET YTGLIKTAML FHNMRRSYFK FQVIATDDYG
KGLSGKADVL VSVVNQLDMQ VIVSNVPPTL VEKKIEDLTE ILDRYVQEQI PGAKVVVESI
GARRHGDAFS LEDYTKCDLT VYAIDPQTNR AIDRNELFKF LDGKLLDINK DFQPYYGEGG
RILEIRTPEA VTSIKKRGES LGYTEGALLA LAFIIILCCI PAILVVLVSY RQFKVRQAEC
TKTARIQAAL PAAKPAVPAP APVAAPPPPP PPPPGAHLYE ELGDSSMHKN YPWSLELILA
RNMDKIITVM SMGMKCLNMG VAVDCYHQLD RRNMVRWLVK LRKNMRRKRK SQRKLKNQRL
KLESLVRRKK *
speed 1.10 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