Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 1.41262538386557e-05 (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 ENST00000414778
Genbank transcript ID NM_001142771
UniProt peptide Q96QU1
alteration type single base exchange
alteration region CDS
DNA changes c.1319A>C
cDNA.1714A>C
g.1432259A>C
AA changes D440A Score: 126 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 440
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      440LRIVALDKDIEDTKDPELHLFLND
mutated  not conserved    440LRIVALDKDIEATKDPELHLFLN
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000009794  435LRIVALDKDIEDTKDPELHLFLN
Fcatus  not conserved  ENSFCAG00000010122  435XXXXXXXXXXXXTKDPELHLFLN
Mmusculus  all identical  ENSMUSG00000052613  440LRIVALDKDIEDTKDPELHLFLN
Ggallus  all conserved  ENSGALG00000002744  383LQITVLDNDVEETKDPQLHLFLN
Trubripes  all conserved  ENSTRUG00000010819  424LEIIALDNDIEETKDPLVKISLD
Drerio  all conserved  ENSDARG00000008127  383LAIIVLDNDIEETKDPMVRISLD
Dmelanogaster  all identical  FBgn0039709  427ISFMTTDADLSDS-DPKPDYIYE
Celegans  not conserved  F15B9.7  415--VKATDEDFGT--
Xtropicalis  all conserved  ENSXETG00000018945  386LKFVALDNDIEETKDPQLYLYLN
protein features
start (aa)end (aa)featuredetails 
271376TOPO_DOMExtracellular (Potential).lost
396509DOMAINCadherin 4.lost
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 5046 / 5046
position (AA) of stopcodon in wt / mu AA sequence 1682 / 1682
position of stopcodon in wt / mu cDNA 5441 / 5441
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 396 / 396
chromosome 10
strand -1
last intron/exon boundary 4890
theoretical NMD boundary in CDS 4444
length of CDS 5046
coding sequence (CDS) position 1319
cDNA position
(for ins/del: last normal base / first normal base)		 1714
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 TCTGGACAAGGACATAGAAGATACAAAAGACCCAGAGCTTC
altered cDNA sequence snippet TCTGGACAAGGACATAGAAGCTACAAAAGACCCAGAGCTTC
wildtype AA sequence MFRQFYLWTC LASGIILGSL FEICLGQYDD GWRYMYCKLA RGGPPATIVA IDEESRNGTI
LVDNMLIKGT AGGPDPTIEL SLKDNVDYWV LMDPVKQMLF LNSTGRVLDR DPPMNIHSIV
VQVQCINKKV GTIIYHEVRI VVRDRNDNSP TFKHESYYAT VNELTPVGTT IFTGFSGDNG
ATDIDDGPNG QIEYVIQYNP DDPTSNDTFE IPLMLTGNIV LRKRLNYEDK TRYFVIIQAN
DRAQNLNERR TTTTTLTVDV LDGDDLGPMF LPCVLVPNTR DCRPLTYQAA IPELRTPEEL
NPIIVTPPIQ AIDQDRNIQP PSDRPGILYS ILVGTPEDYP RFFHMHPRTA ELSLLEPVNR
DFHQKFDLVI KAEQDNGHPL PAFAGLHIEI LDENNQSPYF TMPSYQGYIL ESAPVGATIS
DSLNLTSPLR IVALDKDIED TKDPELHLFL NDYTSVFTVT QTGITRYLTL LQPVDREEQQ
TYTFSITAFD GVQESEPVIV NIQVMDANDN TPTFPEISYD VYVYTDMRPG DSVIQLTAVD
ADEGSNGEIT YEILVGAQGD FIINKTTGLI TIAPGVEMIV GRTYALTVQA ADNAPPAERR
NSICTVYIEV LPPNNQSPPR FPQLMYSLEI SEAMRVGAVL LNLQATDREG DSITYAIENG
DPQRVFNLSE TTGILTLGKA LDRESTDRYI LIITASDGRP DGTSTATVNI VVTDVNDNAP
VFDPYLPRNL SVVEEEANAF VGQVKATDPD AGINGQVHYS LGNFNNLFRI TSNGSIYTAV
KLNREVRDYY ELVVVATDGA VHPRHSTLTL AIKVLDIDDN SPVFTNSTYT VLVEENLPAG
TTILQIEAKD VDLGANVSYR IRSPEVKHFF ALHPFTGELS LLRSLDYEAF PDQEASITFL
VEAFDIYGTM PPGIATVTVI VKDMNDYPPV FSKRIYKGMV APDAVKGTPI TTVYAEDADP
PGLPASRVRY RVDDVQFPYP ASIFEVEEDS GRVITRVNLN EEPTTIFKLV VVAFDDGEPV
MSSSATVKIL VLHPGEIPRF TQEEYRPPPV SELATKGTMV GVISAAAINQ SIVYSIVSGN
EEDTFGINNI TGVIYVNGPL DYETRTSYVL RVQADSLEVV LANLRVPSKS NTAKVYIEIQ
DENNHPPVFQ KKFYIGGVSE DARMFTSVLR VKATDKDTGN YSVMAYRLII PPIKEGKEGF
VVETYTGLIK TAMLFHNMRR SYFKFQVIAT DDYGKGLSGK ADVLVSVVNQ LDMQVIVSNV
PPTLVEKKIE DLTEILDRYV QEQIPGAKVV VESIGARRHG DAFSLEDYTK CDLTVYAIDP
QTNRAIDRNE LFKFLDGKLL DINKDFQPYY GEGGRILEIR TPEAVTSIKK RGESLGYTEG
ALLALAFIII LCCIPAILVV LVSYRQRQAE CTKTARIQAA LPAAKPAVPA PAPVAAPPPP
PPPPPGAHLY EELGDSSILY YRYEMPQYGS RRRLLPPAGQ EEYGEVVGEA EEEYEEEEWA
RKRMIKLVVD REYETSSTGE DSAPECQRNR LHHPSIHSNI NGNIYIAQNG SVVRTRRACL
TDNLKVASPV RLGGPFKKLD KLAVTHEENV PLNTLSKGPF STEKMNARPT LVTFAPCPVG
TDNTAVKPLR NRLKSTVEQE SMIDSKNIKE ALEFHSDHTQ SDDEELWMGP WNNLHIPMTK
L*
mutated AA sequence MFRQFYLWTC LASGIILGSL FEICLGQYDD GWRYMYCKLA RGGPPATIVA IDEESRNGTI
LVDNMLIKGT AGGPDPTIEL SLKDNVDYWV LMDPVKQMLF LNSTGRVLDR DPPMNIHSIV
VQVQCINKKV GTIIYHEVRI VVRDRNDNSP TFKHESYYAT VNELTPVGTT IFTGFSGDNG
ATDIDDGPNG QIEYVIQYNP DDPTSNDTFE IPLMLTGNIV LRKRLNYEDK TRYFVIIQAN
DRAQNLNERR TTTTTLTVDV LDGDDLGPMF LPCVLVPNTR DCRPLTYQAA IPELRTPEEL
NPIIVTPPIQ AIDQDRNIQP PSDRPGILYS ILVGTPEDYP RFFHMHPRTA ELSLLEPVNR
DFHQKFDLVI KAEQDNGHPL PAFAGLHIEI LDENNQSPYF TMPSYQGYIL ESAPVGATIS
DSLNLTSPLR IVALDKDIEA TKDPELHLFL NDYTSVFTVT QTGITRYLTL LQPVDREEQQ
TYTFSITAFD GVQESEPVIV NIQVMDANDN TPTFPEISYD VYVYTDMRPG DSVIQLTAVD
ADEGSNGEIT YEILVGAQGD FIINKTTGLI TIAPGVEMIV GRTYALTVQA ADNAPPAERR
NSICTVYIEV LPPNNQSPPR FPQLMYSLEI SEAMRVGAVL LNLQATDREG DSITYAIENG
DPQRVFNLSE TTGILTLGKA LDRESTDRYI LIITASDGRP DGTSTATVNI VVTDVNDNAP
VFDPYLPRNL SVVEEEANAF VGQVKATDPD AGINGQVHYS LGNFNNLFRI TSNGSIYTAV
KLNREVRDYY ELVVVATDGA VHPRHSTLTL AIKVLDIDDN SPVFTNSTYT VLVEENLPAG
TTILQIEAKD VDLGANVSYR IRSPEVKHFF ALHPFTGELS LLRSLDYEAF PDQEASITFL
VEAFDIYGTM PPGIATVTVI VKDMNDYPPV FSKRIYKGMV APDAVKGTPI TTVYAEDADP
PGLPASRVRY RVDDVQFPYP ASIFEVEEDS GRVITRVNLN EEPTTIFKLV VVAFDDGEPV
MSSSATVKIL VLHPGEIPRF TQEEYRPPPV SELATKGTMV GVISAAAINQ SIVYSIVSGN
EEDTFGINNI TGVIYVNGPL DYETRTSYVL RVQADSLEVV LANLRVPSKS NTAKVYIEIQ
DENNHPPVFQ KKFYIGGVSE DARMFTSVLR VKATDKDTGN YSVMAYRLII PPIKEGKEGF
VVETYTGLIK TAMLFHNMRR SYFKFQVIAT DDYGKGLSGK ADVLVSVVNQ LDMQVIVSNV
PPTLVEKKIE DLTEILDRYV QEQIPGAKVV VESIGARRHG DAFSLEDYTK CDLTVYAIDP
QTNRAIDRNE LFKFLDGKLL DINKDFQPYY GEGGRILEIR TPEAVTSIKK RGESLGYTEG
ALLALAFIII LCCIPAILVV LVSYRQRQAE CTKTARIQAA LPAAKPAVPA PAPVAAPPPP
PPPPPGAHLY EELGDSSILY YRYEMPQYGS RRRLLPPAGQ EEYGEVVGEA EEEYEEEEWA
RKRMIKLVVD REYETSSTGE DSAPECQRNR LHHPSIHSNI NGNIYIAQNG SVVRTRRACL
TDNLKVASPV RLGGPFKKLD KLAVTHEENV PLNTLSKGPF STEKMNARPT LVTFAPCPVG
TDNTAVKPLR NRLKSTVEQE SMIDSKNIKE ALEFHSDHTQ SDDEELWMGP WNNLHIPMTK
L*
speed 1.14 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