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 ENST00000391945
Genbank transcript ID NM_000400
UniProt peptide P18074
alteration type single base exchange
alteration region CDS
DNA changes c.335G>A
cDNA.413G>A
g.2264G>A
AA changes R112H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 112
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      112KLPFLGLALSSRKNLCIHPEVTPL
mutated  not conserved    112KLPFLGLALSSHKNLCIHPE
Ptroglodytes  all identical  ENSPTRG00000011149  112KLPFLGLALSSRKNLCIHPE
Mmulatta  all identical  ENSMMUG00000014419  111KLPFLGLALSSRKNLCIHPEV
Fcatus  all identical  ENSFCAG00000002679  124KLPFLGLALSSRKNLCIHPE
Mmusculus  all identical  ENSMUSG00000030400  112KLPFLGLALSSRKNLCIHPE
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000007303  112SNNFLALALSSRKNLCIHPE
Drerio  all identical  ENSDARG00000021985  112KNDFLALALSSRKNLCIHPE
Dmelanogaster  all identical  FBgn0261850  112PPPFTGLVLSSRKNMCIHPE
Celegans  all identical  Y50D7A.11  112PVAKITVAMSARKNLCVNEP
Xtropicalis  all identical  ENSXETG00000018229  113TLNFMALALSSRRNLCVNPEV
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 2283 / 2283
position (AA) of stopcodon in wt / mu AA sequence 761 / 761
position of stopcodon in wt / mu cDNA 2361 / 2361
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 79 / 79
chromosome 19
strand -1
last intron/exon boundary 2269
theoretical NMD boundary in CDS 2140
length of CDS 2283
coding sequence (CDS) position 335
cDNA position
(for ins/del: last normal base / first normal base)		 413
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 MKLNVDGLLV YFPYDYIYPE QFSYMRELKR TLDAKGHGVL EMPSGTGKTV SLLALIMAYQ
RAYPLEVTKL IYCSRTVPEI EKVIEELRKL LNFYEKQEGE KLPFLGLALS SRKNLCIHPE
VTPLRFGKDV DGKCHSLTAS YVRAQYQHDT SLPHCRFYEE FDAHGREVPL PAGIYNLDDL
KALGRRQGWC PYFLARYSIL HANVVVYSYH YLLDPKIADL VSKELARKAV VVFDEAHNID
NVCIDSMSVN LTRRTLDRCQ GNLETLQKTV LRIKETDEQR LRDEYRRLVE GLREASAARE
TDAHLANPVL PDEVLQEAVP GSIRTAEHFL GFLRRLLEYV KWRLRVQHVV QESPPAFLSG
LAQRVCIQRK PLRFCAERLR SLLHTLEITD LADFSPLTLL ANFATLVSTY AKGFTIIIEP
FDDRTPTIAN PILHFSCMDA SLAIKPVFER FQSVIITSGT LSPLDIYPKI LDFHPVTMAT
FTMTLARVCL CPMIIGRGND QVAISSKFET REDIAVIRNY GNLLLEMSAV VPDGIVAFFT
SYQYMESTVA SWYEQGILEN IQRNKLLFIE TQDGAETSVA LEKYQEACEN GRGAILLSVA
RGKVSEGIDF VHHYGRAVIM FGVPYVYTQS RILKARLEYL RDQFQIREND FLTFDAMRHA
AQCVGRAIRG KTDYGLMVFA DKRFARGDKR GKLPRWIQEH LTDANLNLTV DEGVQVAKYF
LRQMAQPFHR EDQLGLSLLS LEQLESEETL KRIEQIAQQL *
mutated AA sequence MKLNVDGLLV YFPYDYIYPE QFSYMRELKR TLDAKGHGVL EMPSGTGKTV SLLALIMAYQ
RAYPLEVTKL IYCSRTVPEI EKVIEELRKL LNFYEKQEGE KLPFLGLALS SHKNLCIHPE
VTPLRFGKDV DGKCHSLTAS YVRAQYQHDT SLPHCRFYEE FDAHGREVPL PAGIYNLDDL
KALGRRQGWC PYFLARYSIL HANVVVYSYH YLLDPKIADL VSKELARKAV VVFDEAHNID
NVCIDSMSVN LTRRTLDRCQ GNLETLQKTV LRIKETDEQR LRDEYRRLVE GLREASAARE
TDAHLANPVL PDEVLQEAVP GSIRTAEHFL GFLRRLLEYV KWRLRVQHVV QESPPAFLSG
LAQRVCIQRK PLRFCAERLR SLLHTLEITD LADFSPLTLL ANFATLVSTY AKGFTIIIEP
FDDRTPTIAN PILHFSCMDA SLAIKPVFER FQSVIITSGT LSPLDIYPKI LDFHPVTMAT
FTMTLARVCL CPMIIGRGND QVAISSKFET REDIAVIRNY GNLLLEMSAV VPDGIVAFFT
SYQYMESTVA SWYEQGILEN IQRNKLLFIE TQDGAETSVA LEKYQEACEN GRGAILLSVA
RGKVSEGIDF VHHYGRAVIM FGVPYVYTQS RILKARLEYL RDQFQIREND FLTFDAMRHA
AQCVGRAIRG KTDYGLMVFA DKRFARGDKR GKLPRWIQEH LTDANLNLTV DEGVQVAKYF
LRQMAQPFHR EDQLGLSLLS LEQLESEETL KRIEQIAQQL *
speed 1.13 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