Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.610301788013797 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM070925)
  • known disease mutation: rs16778 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:45918128G>CN/A show variant in all transcripts   IGV
HGNC symbol ERCC1
Ensembl transcript ID ENST00000423698
Genbank transcript ID N/A
UniProt peptide P07992
alteration type single base exchange
alteration region CDS
DNA changes c.477C>G
cDNA.577C>G
g.63959C>G
AA changes F159L Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 159
frameshift no
known variant Reference ID: rs121913028
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs16778 (pathogenic for Cerebrooculofacioskeletal syndrome 4|Cockayne syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM070925)

known disease mutation at this position, please check HGMD for details (HGMD ID CM070925)
known disease mutation at this position, please check HGMD for details (HGMD ID CM070925)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1690.995
0.4360.997
(flanking)2.4031
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc lost639680.39wt: GAGCAGGACTTCGTCTCCCGGGTGAGGCCACCTCACCTCCC ccgg|GTGA
distance from splice site 10
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      159ADLLMEKLEQDFVSRVTECLTTVK
mutated  not conserved    159ADLLMEKLEQDLVSRVTECLTTV
Ptroglodytes  all identical  ENSPTRG00000011152  231LMEKLEQDFVSRVTECLTTV
Mmulatta  no homologue    
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000003549  231LMEKLEQNFLSRATECLTTV
Ggallus  no homologue    
Trubripes  all conserved  ENSTRUG00000013151  269LKEQVEKDYLSKVTECLTTV
Drerio  all conserved  ENSDARG00000031680  272LKEQVEKNYLSQVTDCLTTV
Dmelanogaster  not conserved  FBgn0028434  194PDLIMERVESNPHQKLLAALTNI
Celegans  not conserved  F10G8.7  183DDGGDSSMSDERRRNREAAIGFLTAA
Xtropicalis  not conserved  ENSXETG00000026094  197EKDLMSRMAECLTTV
protein features
start (aa)end (aa)featuredetails 
152160HELIXlost
163172STRANDmight get lost (downstream of altered splice site)
175177STRANDmight get lost (downstream of altered splice site)
179192HELIXmight get lost (downstream of altered splice site)
195201STRANDmight get lost (downstream of altered splice site)
202213HELIXmight get lost (downstream of altered splice site)
222226HELIXmight get lost (downstream of altered splice site)
242244STRANDmight get lost (downstream of altered splice site)
247257HELIXmight get lost (downstream of altered splice site)
260264HELIXmight get lost (downstream of altered splice site)
268272HELIXmight get lost (downstream of altered splice site)
274276STRANDmight get lost (downstream of altered splice site)
280290HELIXmight get lost (downstream of altered splice site)
293295STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 678 / 678
position (AA) of stopcodon in wt / mu AA sequence 226 / 226
position of stopcodon in wt / mu cDNA 778 / 778
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 101 / 101
chromosome 19
strand -1
last intron/exon boundary 728
theoretical NMD boundary in CDS 577
length of CDS 678
coding sequence (CDS) position 477
cDNA position
(for ins/del: last normal base / first normal base)		 577
gDNA position
(for ins/del: last normal base / first normal base)		 63959
chromosomal position
(for ins/del: last normal base / first normal base)		 45918128
original gDNA sequence snippet GAGAAGCTAGAGCAGGACTTCGTCTCCCGGGTGAGGCCACC
altered gDNA sequence snippet GAGAAGCTAGAGCAGGACTTGGTCTCCCGGGTGAGGCCACC
original cDNA sequence snippet GAGAAGCTAGAGCAGGACTTCGTCTCCCGGGTGACTGAATG
altered cDNA sequence snippet GAGAAGCTAGAGCAGGACTTGGTCTCCCGGGTGACTGAATG
wildtype AA sequence MDPGKDKEGV PQPSGPPARK KFVIPLDEDE VPPGVRGNPV LKFVRNVPWE FGDVIPDYVL
GQSTCALFLS LRYHNLHPDY IHGRLQSLGK NFALRVLLVQ VDVKDPQQAL KELAKMCILA
DCTLILAWSP EEAGRYLETY KAYEQKPADL LMEKLEQDFV SRVTECLTTV KSVNKTDSQT
LLTTFGSLEQ LIAASREDLA LCPGLGPQKA RRLFDVLHEP FLKVP*
mutated AA sequence MDPGKDKEGV PQPSGPPARK KFVIPLDEDE VPPGVRGNPV LKFVRNVPWE FGDVIPDYVL
GQSTCALFLS LRYHNLHPDY IHGRLQSLGK NFALRVLLVQ VDVKDPQQAL KELAKMCILA
DCTLILAWSP EEAGRYLETY KAYEQKPADL LMEKLEQDLV SRVTECLTTV KSVNKTDSQT
LLTTFGSLEQ LIAASREDLA LCPGLGPQKA RRLFDVLHEP FLKVP*
speed 0.88 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