Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 0.999999923898413 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • 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) chr5:140230370A>CN/A show variant in all transcripts   IGV
HGNC symbol PCDHA6
Ensembl transcript ID ENST00000527624
Genbank transcript ID NM_031849
UniProt peptide Q9UN73
alteration type single base exchange
alteration region intron
DNA changes g.22808A>C
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs369636
databasehomozygous (C/C)heterozygousallele carriers
1000G10709962066
ExAC25467-181677300
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.740.001
-0.6730
(flanking)-0.0210
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased22809wt: 0.8948 / mu: 0.9022 (marginal change - not scored)wt: GGGTAAGCAGAAGAC
mu: GGGTCAGCAGAAGAC		 GTAA|gcag
Donor increased22812wt: 0.26 / mu: 0.56wt: TAAGCAGAAGACCGA
mu: TCAGCAGAAGACCGA		 AGCA|gaag
Donor increased22799wt: 0.52 / mu: 0.77wt: GCTCTGGCGAGGGTA
mu: GCTCTGGCGAGGGTC		 TCTG|gcga
distance from splice site 21092
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes		 N/A
protein features
start (aa)end (aa)featuredetails 
30697TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
456565DOMAINCadherin 5.might get lost (downstream of altered splice site)
548548CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
581678DOMAINCadherin 6.might get lost (downstream of altered splice site)
698718TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
719950TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
799802REPEATPXXP 1.might get lost (downstream of altered splice site)
799894REGION4 X 4 AA repeats of P-X-X-P.might get lost (downstream of altered splice site)
832835REPEATPXXP 2.might get lost (downstream of altered splice site)
873876REPEATPXXP 3.might get lost (downstream of altered splice site)
891894REPEATPXXP 4.might get lost (downstream of altered splice site)
923930COMPBIASPoly-Lys.might get lost (downstream of altered splice site)
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 28 / 28
chromosome 5
strand 1
last intron/exon boundary 1778
theoretical NMD boundary in CDS 1700
length of CDS 2061
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)		 22808
chromosomal position
(for ins/del: last normal base / first normal base)		 140230370
original gDNA sequence snippet GGGTGTGCTCTGGCGAGGGTAAGCAGAAGACCGACCTCATG
altered gDNA sequence snippet GGGTGTGCTCTGGCGAGGGTCAGCAGAAGACCGACCTCATG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MVFTPEDRLG KQCLLLPLLL LAAWKVGSGQ LHYSVPEEAK HGTFVGRIAQ DLGLELAELV
PRLFRMASKD REDLLEVNLQ NGILFVNSRI DREELCGRSA ECSIHLEVIV DRPLQVFHVD
VEVRDINDNP PLFPVEEQRV LIYESRLPDS VFPLEGASDA DVGSNSILTY KLSSSEYFGL
DVKINSDDNK QIGLLLKKSL DREEAPAHNL FLTATDGGKP ELTGTVQLLV TVLDVNDNAP
TFEQSEYEVR IFENADNGTT VIRLNASDRD EGANGAISYS FNSLVAAMVI DHFSIDRNTG
EIVIRGNLDF EQENLYKILI DATDKGHPPM AGHCTVLVRI LDKNDNVPEI ALTSLSLPVR
EDAQFGTVIA LISVNDLDSG ANGQVNCSLT PHVPFKLVST FKNYYSLVLD SALDRESVSA
YELVVTARDG GSPSLWATAS LSVEVADMND NAPAFAQPEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRVG ERALSSYISV HAESGKVYAL QPLDHEELEL LQFQPRQPNP
DWRYSASLRA GMHSSVHLEE AGILRAGPGG PDQQWPTVSS ATPEPEAGEV SPPVGAGVNS
NSWTFKYGPG NPKQSGPGEL PDKFIIPGSP AIISIRQEPT NSQIDKSDFI TFGKKEETKK
KKKKKKGNKT QEKKEKGNST TDNSDQ*
mutated AA sequence N/A
speed 0.46 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