Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999993293996 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM010231)
  • known disease mutation at this position (HGMD CM136294)
  • known disease mutation: rs16787 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:45855769C>TN/A show variant in all transcripts   IGV
HGNC symbol ERCC2
Ensembl transcript ID ENST00000391944
Genbank transcript ID N/A
UniProt peptide P18074
alteration type single base exchange
alteration region CDS
DNA changes c.1807G>A
cDNA.1835G>A
g.18408G>A
AA changes D603N Score: 23 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 603
frameshift no
known variant Reference ID: rs121913023
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs16787 (pathogenic for Cerebrooculofacioskeletal syndrome 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM010231)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010231)
known disease mutation at this position, please check HGMD for details (HGMD ID CM136294)

known disease mutation at this position, please check HGMD for details (HGMD ID CM010231)
known disease mutation at this position, please check HGMD for details (HGMD ID CM136294)
known disease mutation at this position, please check HGMD for details (HGMD ID CM010231)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.2471
5.1381
(flanking)-1.8830.156
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased18408wt: 0.8083 / mu: 0.8335 (marginal change - not scored)wt: ACGGCCTCATGGTCTTTGCCGACAAGGTGCAGCTTCAGGGG
mu: ACGGCCTCATGGTCTTTGCCAACAAGGTGCAGCTTCAGGGG		 gccg|ACAA
Donor increased18412wt: 0.31 / mu: 0.56wt: CGACAAGGTGCAGCT
mu: CAACAAGGTGCAGCT		 ACAA|ggtg
Donor marginally increased18408wt: 0.8770 / mu: 0.9447 (marginal change - not scored)wt: TTGCCGACAAGGTGC
mu: TTGCCAACAAGGTGC		 GCCG|acaa
Donor gained184040.71mu: GTCTTTGCCAACAAG CTTT|gcca
distance from splice site 6
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      603GKTDYGLMVFADKRFARGDKRGKL
mutated  all conserved    603FANKRFARGDKRGK
Ptroglodytes  all identical  ENSPTRG00000011149  681GKTDYGLMVFADKRFARGDKRGK
Mmulatta  all identical  ENSMMUG00000014419  678GKTDYGLMVFADKRFARGDKRGK
Fcatus  all identical  ENSFCAG00000002679  693GKTDYGLMVFADKRFARADKRGK
Mmusculus  all identical  ENSMUSG00000030400  681GKTDYGLMVFADKRFARADKRGK
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000007303  681FADKRYARADKRGK
Drerio  all identical  ENSDARG00000021985  681FADKRYARADKRGK
Dmelanogaster  all identical  FBgn0261850  681FADKRFSRHDKRSR
Celegans  no alignment  Y50D7A.11  n/a
Xtropicalis  all identical  ENSXETG00000018229  680GKTDYGIMLFADKRYARSDKRGK
protein features
start (aa)end (aa)featuredetails 
438637REGIONMediates interaction with MMS19.lost
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 2049 / 2049
position (AA) of stopcodon in wt / mu AA sequence 683 / 683
position of stopcodon in wt / mu cDNA 2077 / 2077
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 29 / 29
chromosome 19
strand -1
last intron/exon boundary 1985
theoretical NMD boundary in CDS 1906
length of CDS 2049
coding sequence (CDS) position 1807
cDNA position
(for ins/del: last normal base / first normal base)		 1835
gDNA position
(for ins/del: last normal base / first normal base)		 18408
chromosomal position
(for ins/del: last normal base / first normal base)		 45855769
original gDNA sequence snippet ACGGCCTCATGGTCTTTGCCGACAAGGTGCAGCTTCAGGGG
altered gDNA sequence snippet ACGGCCTCATGGTCTTTGCCAACAAGGTGCAGCTTCAGGGG
original cDNA sequence snippet ACGGCCTCATGGTCTTTGCCGACAAGCGGTTTGCCCGTGGG
altered cDNA sequence snippet ACGGCCTCATGGTCTTTGCCAACAAGCGGTTTGCCCGTGGG
wildtype AA sequence MKLNVDGLLV YFPYDYIYPE QFSYMRELKR TLDAKGHGVL EMPSGTGKTV SLLALIMAYQ
RAYPLEVTKL IYCSRTVPEI EKVIEELRKL LNFYEKQEGE KLPFLGLALS SRKNLCIHPE
ILHANVVVYS YHYLLDPKIA DLVSKELARK AVVVFDEAHN IDNVCIDSMS VNLTRRTLDR
CQGNLETLQK TVLRIKETDE QRLRDEYRRL VEGLREASAA RETDAHLANP VLPDEVLQEA
VPGSIRTAEH FLGFLRRLLE YVKWRLRVQH VVQESPPAFL SGLAQRVCIQ RKPLRFCAER
LRSLLHTLEI TDLADFSPLT LLANFATLVS TYAKGFTIII EPFDDRTPTI ANPILHFSCM
DASLAIKPVF ERFQSVIITS GTLSPLDIYP KILDFHPVTM ATFTMTLARV CLCPMIIGRG
NDQVAISSKF ETREDIAVIR NYGNLLLEMS AVVPDGIVAF FTSYQYMEST VASWYEQGIL
ENIQRNKLLF IETQDGAETS VALEKYQEAC ENGRGAILLS VARGKVSEGI DFVHHYGRAV
IMFGVPYVYT QSRILKARLE YLRDQFQIRE NDFLTFDAMR HAAQCVGRAI RGKTDYGLMV
FADKRFARGD KRGKLPRWIQ EHLTDANLNL TVDEGVQVAK YFLRQMAQPF HREDQLGLSL
LSLEQLESEE TLKRIEQIAQ QL*
mutated AA sequence MKLNVDGLLV YFPYDYIYPE QFSYMRELKR TLDAKGHGVL EMPSGTGKTV SLLALIMAYQ
RAYPLEVTKL IYCSRTVPEI EKVIEELRKL LNFYEKQEGE KLPFLGLALS SRKNLCIHPE
ILHANVVVYS YHYLLDPKIA DLVSKELARK AVVVFDEAHN IDNVCIDSMS VNLTRRTLDR
CQGNLETLQK TVLRIKETDE QRLRDEYRRL VEGLREASAA RETDAHLANP VLPDEVLQEA
VPGSIRTAEH FLGFLRRLLE YVKWRLRVQH VVQESPPAFL SGLAQRVCIQ RKPLRFCAER
LRSLLHTLEI TDLADFSPLT LLANFATLVS TYAKGFTIII EPFDDRTPTI ANPILHFSCM
DASLAIKPVF ERFQSVIITS GTLSPLDIYP KILDFHPVTM ATFTMTLARV CLCPMIIGRG
NDQVAISSKF ETREDIAVIR NYGNLLLEMS AVVPDGIVAF FTSYQYMEST VASWYEQGIL
ENIQRNKLLF IETQDGAETS VALEKYQEAC ENGRGAILLS VARGKVSEGI DFVHHYGRAV
IMFGVPYVYT QSRILKARLE YLRDQFQIRE NDFLTFDAMR HAAQCVGRAI RGKTDYGLMV
FANKRFARGD KRGKLPRWIQ EHLTDANLNL TVDEGVQVAK YFLRQMAQPF HREDQLGLSL
LSLEQLESEE TLKRIEQIAQ QL*
speed 0.13 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