Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999992277747 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM1610826)
  • known disease mutation at this position (HGMD CM972918)
  • known disease mutation: rs16788 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:45856060G>AN/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.1846C>T
cDNA.1924C>T
g.18117C>T
AA changes R616W Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 616
frameshift no
known variant Reference ID: rs121913024
databasehomozygous (A/A)heterozygousallele carriers
1000G---
ExAC066

known disease mutation: rs16788 (pathogenic for Xeroderma pigmentosum, group D|Cerebrooculofacioskeletal syndrome 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM1610826)

known disease mutation at this position, please check HGMD for details (HGMD ID CM1610826)
known disease mutation at this position, please check HGMD for details (HGMD ID CM972918)

known disease mutation at this position, please check HGMD for details (HGMD ID CM1610826)
known disease mutation at this position, please check HGMD for details (HGMD ID CM972918)
known disease mutation at this position, please check HGMD for details (HGMD ID CM972918)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.3911
3.7861
(flanking)0.2390.998
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 15
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      616SEGIDFVHHYGRAVIMFGVPYVYT
mutated  not conserved    616SEGIDFVHHYGWAVIMFGVPYVY
Ptroglodytes  all identical  ENSPTRG00000011149  616SEGIDFVHHYGRAVIMFGVPYVY
Mmulatta  all identical  ENSMMUG00000014419  613SDGIHFMHHYGRAVIMFGVPYVY
Fcatus  all identical  ENSFCAG00000002679  628SEGIDFVHHYGRAVIMFGVPYVY
Mmusculus  all identical  ENSMUSG00000030400  616SEGIDFVHHYGRAVIMFGVPYVY
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000007303  616SEGIDFVHHFGRAVIMFGVPYVY
Drerio  all identical  ENSDARG00000021985  616SEGIDFVHHFGRAVIMFGVPYVY
Dmelanogaster  all identical  FBgn0261850  616SEGVDFDHHYGRAVLMFGIPYVY
Celegans  no alignment  Y50D7A.11  n/a
Xtropicalis  all identical  ENSXETG00000018229  615SEGIDFVHHYGRAVIMFGVPYVY
protein features
start (aa)end (aa)featuredetails 
438637REGIONMediates interaction with MMS19.lost
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 1846
cDNA position
(for ins/del: last normal base / first normal base)		 1924
gDNA position
(for ins/del: last normal base / first normal base)		 18117
chromosomal position
(for ins/del: last normal base / first normal base)		 45856060
original gDNA sequence snippet CACCAGTGCACCACTACGGGCGGGCCGTCATCATGTTTGGC
altered gDNA sequence snippet CACCAGTGCACCACTACGGGTGGGCCGTCATCATGTTTGGC
original cDNA sequence snippet ACTTTGTGCACCACTACGGGCGGGCCGTCATCATGTTTGGC
altered cDNA sequence snippet ACTTTGTGCACCACTACGGGTGGGCCGTCATCATGTTTGGC
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 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 VHHYGWAVIM FGVPYVYTQS RILKARLEYL RDQFQIREND FLTFDAMRHA
AQCVGRAIRG KTDYGLMVFA DKRFARGDKR GKLPRWIQEH LTDANLNLTV DEGVQVAKYF
LRQMAQPFHR EDQLGLSLLS LEQLESEETL KRIEQIAQQL *
speed 1.29 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