Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: simple_aae, prob: 1.65400571018668e-06 (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 ENST00000373965
Genbank transcript ID NM_001142772
UniProt peptide Q96QU1
alteration type single base exchange
alteration region CDS
DNA changes c.1304A>C
cDNA.1699A>C
g.1432259A>C
AA changes D435A Score: 126 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 435
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      435LRIVALDKDIEDVPPSGVPTKDPE
mutated  not conserved    435LRIVALDKDIEAVPPSGVPTKDP
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000009794  435LRIVALDKDIED-------TKDP
Fcatus  not conserved  ENSFCAG00000010122  435XXXXXXXXXXXX-------TKDP
Mmusculus  all identical  ENSMUSG00000052613  440LRIVALDKDIED-------TKDP
Ggallus  all conserved  ENSGALG00000002744  383LQITVLDNDVEE-------TKDP
Trubripes  all conserved  ENSTRUG00000010819  424E-------TKDP
Drerio  all conserved  ENSDARG00000008127  383LAIIVLDNDIEE-------TKDP
Dmelanogaster  all identical  FBgn0039709  427ISFMTTDADLSD--------SDP
Celegans  all identical  F15B9.7  415AVIATVKATDEDFG
Xtropicalis  all conserved  ENSXETG00000018945  386LKFVALDNDIEE-------TKDP
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 5055 / 5055
position (AA) of stopcodon in wt / mu AA sequence 1685 / 1685
position of stopcodon in wt / mu cDNA 5450 / 5450
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 4899
theoretical NMD boundary in CDS 4453
length of CDS 5055
coding sequence (CDS) position 1304
cDNA position
(for ins/del: last normal base / first normal base)		 1699
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 MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPTS NDTFEIPLML TGNIVLRKRL NYEDKTRYFV IIQANDRAQN
LNERRTTTTT LTVDVLDGDD LGPMFLPCVL VPNTRDCRPL TYQAAIPELR TPEELNPIIV
TPPIQAIDQD RNIQPPSDRP GILYSILVGT PEDYPRFFHM HPRTAELSLL EPVNRDFHQK
FDLVIKAEQD NGHPLPAFAG LHIEILDENN QSPYFTMPSY QGYILESAPV GATISDSLNL
TSPLRIVALD KDIEDVPPSG VPTKDPELHL FLNDYTSVFT VTQTGITRYL TLLQPVDREE
QQTYTFSITA FDGVQESEPV IVNIQVMDAN DNTPTFPEIS YDVYVYTDMR PGDSVIQLTA
VDADEGSNGE ITYEILVGAQ GDFIINKTTG LITIAPGVEM IVGRTYALTV QAADNAPPAE
RRNSICTVYI EVLPPNNQSP PRFPQLMYSL EISEAMRVGA VLLNLQATDR EGDSITYAIE
NGDPQRVFNL SETTGILTLG KALDRESTDR YILIITASDG RPDGTSTATV NIVVTDVNDN
APVFDPYLPR NLSVVEEEAN AFVGQVKATD PDAGINGQVH YSLGNFNNLF RITSNGSIYT
AVKLNREVRD YYELVVVATD GAVHPRHSTL TLAIKVLDID DNSPVFTNST YTVLVEENLP
AGTTILQIEA KDVDLGANVS YRIRSPEVKH FFALHPFTGE LSLLRSLDYE AFPDQEASIT
FLVEAFDIYG TMPPGIATVT VIVKDMNDYP PVFSKRIYKG MVAPDAVKGT PITTVYAEDA
DPPGLPASRV RYRVDDVQFP YPASIFEVEE DSGRVITRVN LNEEPTTIFK LVVVAFDDGE
PVMSSSATVK ILVLHPGEIP RFTQEEYRPP PVSELATKGT MVGVISAAAI NQSIVYSIVS
GNEEDTFGIN NITGVIYVNG PLDYETRTSY VLRVQADSLE VVLANLRVPS KSNTAKVYIE
IQDENNHPPV FQKKFYIGGV SEDARMFTSV LRVKATDKDT GNYSVMAYRL IIPPIKEGKE
GFVVETYTGL IKTAMLFHNM RRSYFKFQVI ATDDYGKGLS GKADVLVSVV NQLDMQVIVS
NVPPTLVEKK IEDLTEILDR YVQEQIPGAK VVVESIGARR HGDAFSLEDY TKCDLTVYAI
DPQTNRAIDR NELFKFLDGK LLDINKDFQP YYGEGGRILE IRTPEAVTSI KKRGESLGYT
EGALLALAFI IILCCIPAIL VVLVSYRQFK VRQAECTKTA RIQAALPAAK PAVPAPAPVA
APPPPPPPPP GAHLYEELGD SSMHKYEMPQ YGSRRRLLPP AGQEEYGEVV GEAEEEYEEE
EWARKRMIKL VVDREYETSS TGEDSAPECQ RNRLHHPSIH SNINGNIYIA QNGSVVRTRR
ACLTDNLKVA SPVRLGGPFK KLDKLAVTHE ENVPLNTLSK GPFSTEKMNA RPTLVTFAPC
PVGTDNTAVK PLRNRLKSTV EQESMIDSKN IKEALEFHSD HTQSDDEELW MGPWNNLHIP
MTKL*
mutated AA sequence MFRQFYLWTC LASGIILGSL FEICLGQYDD DCKLARGGPP ATIVAIDEES RNGTILVDNM
LIKGTAGGPD PTIELSLKDN VDYWVLMDPV KQMLFLNSTG RVLDRDPPMN IHSIVVQVQC
INKKVGTIIY HEVRIVVRDR NDNSPTFKHE SYYATVNELT PVGTTIFTGF SGDNGATDID
DGPNGQIEYV IQYNPDDPTS NDTFEIPLML TGNIVLRKRL NYEDKTRYFV IIQANDRAQN
LNERRTTTTT LTVDVLDGDD LGPMFLPCVL VPNTRDCRPL TYQAAIPELR TPEELNPIIV
TPPIQAIDQD RNIQPPSDRP GILYSILVGT PEDYPRFFHM HPRTAELSLL EPVNRDFHQK
FDLVIKAEQD NGHPLPAFAG LHIEILDENN QSPYFTMPSY QGYILESAPV GATISDSLNL
TSPLRIVALD KDIEAVPPSG VPTKDPELHL FLNDYTSVFT VTQTGITRYL TLLQPVDREE
QQTYTFSITA FDGVQESEPV IVNIQVMDAN DNTPTFPEIS YDVYVYTDMR PGDSVIQLTA
VDADEGSNGE ITYEILVGAQ GDFIINKTTG LITIAPGVEM IVGRTYALTV QAADNAPPAE
RRNSICTVYI EVLPPNNQSP PRFPQLMYSL EISEAMRVGA VLLNLQATDR EGDSITYAIE
NGDPQRVFNL SETTGILTLG KALDRESTDR YILIITASDG RPDGTSTATV NIVVTDVNDN
APVFDPYLPR NLSVVEEEAN AFVGQVKATD PDAGINGQVH YSLGNFNNLF RITSNGSIYT
AVKLNREVRD YYELVVVATD GAVHPRHSTL TLAIKVLDID DNSPVFTNST YTVLVEENLP
AGTTILQIEA KDVDLGANVS YRIRSPEVKH FFALHPFTGE LSLLRSLDYE AFPDQEASIT
FLVEAFDIYG TMPPGIATVT VIVKDMNDYP PVFSKRIYKG MVAPDAVKGT PITTVYAEDA
DPPGLPASRV RYRVDDVQFP YPASIFEVEE DSGRVITRVN LNEEPTTIFK LVVVAFDDGE
PVMSSSATVK ILVLHPGEIP RFTQEEYRPP PVSELATKGT MVGVISAAAI NQSIVYSIVS
GNEEDTFGIN NITGVIYVNG PLDYETRTSY VLRVQADSLE VVLANLRVPS KSNTAKVYIE
IQDENNHPPV FQKKFYIGGV SEDARMFTSV LRVKATDKDT GNYSVMAYRL IIPPIKEGKE
GFVVETYTGL IKTAMLFHNM RRSYFKFQVI ATDDYGKGLS GKADVLVSVV NQLDMQVIVS
NVPPTLVEKK IEDLTEILDR YVQEQIPGAK VVVESIGARR HGDAFSLEDY TKCDLTVYAI
DPQTNRAIDR NELFKFLDGK LLDINKDFQP YYGEGGRILE IRTPEAVTSI KKRGESLGYT
EGALLALAFI IILCCIPAIL VVLVSYRQFK VRQAECTKTA RIQAALPAAK PAVPAPAPVA
APPPPPPPPP GAHLYEELGD SSMHKYEMPQ YGSRRRLLPP AGQEEYGEVV GEAEEEYEEE
EWARKRMIKL VVDREYETSS TGEDSAPECQ RNRLHHPSIH SNINGNIYIA QNGSVVRTRR
ACLTDNLKVA SPVRLGGPFK KLDKLAVTHE ENVPLNTLSK GPFSTEKMNA RPTLVTFAPC
PVGTDNTAVK PLRNRLKSTV EQESMIDSKN IKEALEFHSD HTQSDDEELW MGPWNNLHIP
MTKL*
speed 1.49 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