Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999906870434 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • heterozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM940373)
  • known disease mutation: rs16779 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr19:45860626G>CN/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.1381C>G
cDNA.1459C>G
g.13551C>G
AA changes L461V Score: 32 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 461
frameshift no
known variant Reference ID: rs121913016
databasehomozygous (C/C)heterozygousallele carriers
1000G077
ExAC2158160

known disease mutation: rs16779 (pathogenic for Xeroderma pigmentosum, group D|Trichothiodystrophy 1, photosensitive|not specified|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM940373)

known disease mutation at this position, please check HGMD for details (HGMD ID CM940373)
known disease mutation at this position, please check HGMD for details (HGMD ID CM940373)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.91
4.6960.998
(flanking)-3.2670.007
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 increased13547wt: 0.6189 / mu: 0.6298 (marginal change - not scored)wt: CCTCCCACTGTCCCGCCACAGACACTGTCCCCGCTGGACAT
mu: CCTCCCACTGTCCCGCCACAGACAGTGTCCCCGCTGGACAT		 acag|ACAC
Acc marginally increased13544wt: 0.3281 / mu: 0.3550 (marginal change - not scored)wt: ATCCCTCCCACTGTCCCGCCACAGACACTGTCCCCGCTGGA
mu: ATCCCTCCCACTGTCCCGCCACAGACAGTGTCCCCGCTGGA		 gcca|CAGA
Donor gained135500.48mu: CAGACAGTGTCCCCG GACA|gtgt
Donor gained135470.43mu: CCACAGACAGTGTCC ACAG|acag
distance from splice site 4
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      461RFQSVIITSGTLSPLDIYPKILDF
mutated  all conserved    461RFQSVIITSGTVSPLDIYPKILD
Ptroglodytes  all identical  ENSPTRG00000011149  461RFQSVIITSGTLSPLDIYPKILD
Mmulatta  all identical  ENSMMUG00000014419  459RFQSVIITSGTLSPLDIYPKILD
Fcatus  all identical  ENSFCAG00000002679  473RFQSVIITSGTLSPLDIYPKILD
Mmusculus  all identical  ENSMUSG00000030400  461RFQSVIITSGTLSPLDIYPKILD
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000007303  461RFQSVVITSGTLSPLDIYPKILD
Drerio  all identical  ENSDARG00000021985  461RFQTVIITSGTLSPLDIYPRILD
Dmelanogaster  all identical  FBgn0261850  461RFQTVVITSGTLSPMDMYPKILD
Celegans  no alignment  Y50D7A.11  n/a
Xtropicalis  all identical  ENSXETG00000018229  462FLPIFGLISFFLARRNDF---LP
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 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 1381
cDNA position
(for ins/del: last normal base / first normal base)		 1459
gDNA position
(for ins/del: last normal base / first normal base)		 13551
chromosomal position
(for ins/del: last normal base / first normal base)		 45860626
original gDNA sequence snippet CCACTGTCCCGCCACAGACACTGTCCCCGCTGGACATCTAC
altered gDNA sequence snippet CCACTGTCCCGCCACAGACAGTGTCCCCGCTGGACATCTAC
original cDNA sequence snippet TCATCATCACATCTGGGACACTGTCCCCGCTGGACATCTAC
altered cDNA sequence snippet TCATCATCACATCTGGGACAGTGTCCCCGCTGGACATCTAC
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 VSPLDIYPKI 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 1.10 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