Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999998067059 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM940372)
  • known disease mutation: rs16784 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:45871913C>TN/A show variant in all transcripts   IGV
HGNC symbol ERCC2
Ensembl transcript ID ENST00000485403
Genbank transcript ID N/A
UniProt peptide P18074
alteration type single base exchange
alteration region CDS
DNA changes c.263G>A
cDNA.482G>A
g.2264G>A
AA changes R88H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 88
frameshift no
known variant Reference ID: rs121913020
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC033

known disease mutation: rs16784 (pathogenic for Xeroderma pigmentosum, group D|Trichothiodystrophy 1, photosensitive|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940372)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940372)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940372)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.860.699
5.2150.997
(flanking)0.8270.996
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased2264wt: 0.28 / mu: 0.46wt: CTCCCGCAAAAACTT
mu: CTCCCACAAAAACTT		 CCCG|caaa
Donor increased2265wt: 0.21 / mu: 0.28wt: TCCCGCAAAAACTTG
mu: TCCCACAAAAACTTG		 CCGC|aaaa
Donor gained22620.54mu: AGCTCCCACAAAAAC CTCC|caca
distance from splice site 26
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      88KLPFLGLALSSRKNLCIHPEVTPL
mutated  not conserved    88KLPFLGLALSSHKNLCIHPEVTP
Ptroglodytes  all identical  ENSPTRG00000011149  112KLPFLGLALSSRKNLCIHPEVTP
Mmulatta  all identical  ENSMMUG00000014419  111KLPFLGLALSSRKNLCIHPEVTP
Fcatus  all identical  ENSFCAG00000002679  124KLPFLGLALSSRKNLCIHPE
Mmusculus  all identical  ENSMUSG00000030400  112KLPFLGLALSSRKNLCIHPEVTP
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000007303  112SNNFLALALSSRKNLCIHPEVSA
Drerio  all identical  ENSDARG00000021985  112KNDFLALALSSRKNLCIHPEVSS
Dmelanogaster  all identical  FBgn0261850  112PPPFTGLVLSSRKNMCIHPEVSK
Celegans  all identical  Y50D7A.11  112PVAKITVAMSARKNLCVNEPVAA
Xtropicalis  all identical  ENSXETG00000018229  113TLNFMALALSSRRNLCVNPEVSA
protein features
start (aa)end (aa)featuredetails 
7283DOMAINHelicase ATP-binding.lost
116116METALIron-sulfur (4Fe-4S) (By similarity).might get lost (downstream of altered splice site)
134134METALIron-sulfur (4Fe-4S) (By similarity).might get lost (downstream of altered splice site)
155155METALIron-sulfur (4Fe-4S) (By similarity).might get lost (downstream of altered splice site)
190190METALIron-sulfur (4Fe-4S) (Probable).might get lost (downstream of altered splice site)
190190MUTAGENC->S: Reduced iron-sulfur-binding. Iron- sulfur-binding is further decreased in absence of MMS19.might get lost (downstream of altered splice site)
234237MOTIFDEAH box.might get lost (downstream of altered splice site)
438637REGIONMediates interaction with MMS19.might get lost (downstream of altered splice site)
682695MOTIFNuclear localization signal (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1218 / 1218
position (AA) of stopcodon in wt / mu AA sequence 406 / 406
position of stopcodon in wt / mu cDNA 1437 / 1437
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 220 / 220
chromosome 19
strand -1
last intron/exon boundary 1385
theoretical NMD boundary in CDS 1115
length of CDS 1218
coding sequence (CDS) position 263
cDNA position
(for ins/del: last normal base / first normal base)		 482
gDNA position
(for ins/del: last normal base / first normal base)		 2264
chromosomal position
(for ins/del: last normal base / first normal base)		 45871913
original gDNA sequence snippet GGGACTGGCTCTGAGCTCCCGCAAAAACTTGTGTATTCACC
altered gDNA sequence snippet GGGACTGGCTCTGAGCTCCCACAAAAACTTGTGTATTCACC
original cDNA sequence snippet GGGACTGGCTCTGAGCTCCCGCAAAAACTTGTGTATTCACC
altered cDNA sequence snippet GGGACTGGCTCTGAGCTCCCACAAAAACTTGTGTATTCACC
wildtype AA sequence MRELKRTLDA KGHGVLEMPS GTGKTVSLLA LIMAYQRAYP LEVTKLIYCS RTVPEIEKVI
EELRKLLNFY EKQEGEKLPF LGLALSSRKN LCIHPEVTPL RFGKDVDGKC HSLTASYVRA
QYQHDTSLPH CRFYEEFDAH GREVPLPAGI YNLDDLKALG RRQGWCPYFL ARYSILHANV
VVYSYHYLLD PKIADLVSKE LARKAVVVFD EAHNIDNVCI DSMSVNLTRR TLDRCQGNLE
TLQKTVLRIK ETDEQRLRDE YRRLVEGLRE ASAARETDAH LANPVLPDEV LQEAVPGSIR
TAEHFLGFLR RLLEYVKWRL RVQHVVQESP PAFLSGLAQR VCIQRKPLRF CAERLRSLLH
TLEITDLADF SPLTLLANFA TLVSTYAKGQ AQHCGSSRNQ KRSHP*
mutated AA sequence MRELKRTLDA KGHGVLEMPS GTGKTVSLLA LIMAYQRAYP LEVTKLIYCS RTVPEIEKVI
EELRKLLNFY EKQEGEKLPF LGLALSSHKN LCIHPEVTPL RFGKDVDGKC HSLTASYVRA
QYQHDTSLPH CRFYEEFDAH GREVPLPAGI YNLDDLKALG RRQGWCPYFL ARYSILHANV
VVYSYHYLLD PKIADLVSKE LARKAVVVFD EAHNIDNVCI DSMSVNLTRR TLDRCQGNLE
TLQKTVLRIK ETDEQRLRDE YRRLVEGLRE ASAARETDAH LANPVLPDEV LQEAVPGSIR
TAEHFLGFLR RLLEYVKWRL RVQHVVQESP PAFLSGLAQR VCIQRKPLRF CAERLRSLLH
TLEITDLADF SPLTLLANFA TLVSTYAKGQ AQHCGSSRNQ KRSHP*
speed 0.53 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