Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

polymorphism

 Model: without_aae, prob: 2.58899940659565e-11 (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) chr5:140182101G>TN/A show variant in all transcripts   IGV
HGNC symbol PCDHA1
Ensembl transcript ID ENST00000394633
Genbank transcript ID NM_031411
UniProt peptide Q9Y5I3
alteration type single base exchange
alteration region intron
DNA changes g.16226G>T
AA changes N/A
position(s) of altered AA
if AA alteration in CDS		 N/A
frameshift N/A
known variant Reference ID: rs7701755
databasehomozygous (T/T)heterozygousallele carriers
1000G91011422052
ExAC18302-383714465
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me3, Histone, Histone 3 Lysine 9 Tri-Methylation
H3K79me3, Histone, Histone 3 Lysine 79 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)2.160.992
1.2080.987
(flanking)0.3230.959
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc gained162370.42mu: CCACGGCCATCGTGTCCGTGGAGGTGGCCGACGTGAACGAC gtgg|AGGT
distance from splice site 14624
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)
588678DOMAINCadherin 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)
734737REPEATPXXP 1.might get lost (downstream of altered splice site)
734894REGION5 X 4 AA repeats of P-X-X-P.might get lost (downstream of altered splice site)
799802REPEATPXXP 2.might get lost (downstream of altered splice site)
832835REPEATPXXP 3.might get lost (downstream of altered splice site)
873876REPEATPXXP 4.might get lost (downstream of altered splice site)
891894REPEATPXXP 5.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 1 / 1
chromosome 5
strand 1
last intron/exon boundary 1751
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)		 16226
chromosomal position
(for ins/del: last normal base / first normal base)		 140182101
original gDNA sequence snippet TTCACTGTGGGCCACGGCCAGCGTGTCCGTGGAGGTGGCCG
altered gDNA sequence snippet TTCACTGTGGGCCACGGCCATCGTGTCCGTGGAGGTGGCCG
original cDNA sequence snippet N/A
altered cDNA sequence snippet N/A
wildtype AA sequence MVFSRRGGLG ARDLLLWLLL LAAWEVGSGQ LHYSIPEEAK HGTFVGRVAQ DLGLELAELV
PRLFRVASKT HRDLLEVNLQ NGILFVNSRI DREELCQWSA ECSIHLELIA DRPLQVFHVE
VKVKDINDNP PVFRGREQII FIPESRLLNS RFPIEGAADA DIGANALLTY TLSPSDYFSL
DVEASDELSK SLWLELRKYL DREETPELHL LLTATDGGKP ELQGTVELLI TVLDVNDNAP
LFDQAVYRVH LLETTANGTL VTTLNASDAD EGVNGEVVFS FDSGISRDIQ EKFKVDSSSG
EIRLIDKLDY EETKSYEIQV KAVDKGSPPM SNHCKVLVKV LDVNDNAPEL AVTSLYLPIR
EDAPLSTVIA LITVSDRDSG ANGQVTCSLM PHVPFKLVST FKNYYSLVLD SALDRESLSV
YELVVTARDG GSPSLWATAR VSVEVADVND NAPAFAQPEY TVFVKENNPP GCHIFTVSAR
DADAQENALV SYSLVERRVG ERALSNYVSV HAESGKVYAL QPLDHEELEL LQFQPRQPNP
DWRYSASLRA GMHSSVHLEE AGILRAGPGG PDQQWPTVSS ATPEPEAGEV SPPVGAGVNS
NSWTFKYGPG NPKQSGPGEL PDKFIIPGSP AIISIRQEPT NSQIDKSDFI TFGKKEETKK
KKKKKKGNKT QEKKEKGNST TDNSDQ*
mutated AA sequence N/A
speed 0.73 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