Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000391945
Querying Taster for transcript #2: ENST00000391944
MT speed 3.85 s - this script 6.233643 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ERCC2disease_causing_automatic0.999999991268223simple_aaeaffected0D681Nsingle base exchangers121913023show file
ERCC2disease_causing_automatic0.999999993293996simple_aaeaffected0D603Nsingle base exchangers121913023show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999991268223 (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 ENST00000391945
Genbank transcript ID NM_000400
UniProt peptide P18074
alteration type single base exchange
alteration region CDS
DNA changes c.2041G>A
cDNA.2119G>A
g.18408G>A
AA changes D681N Score: 23 explain score(s)
position(s) of altered AA
if AA alteration in CDS
681
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 marginally increased18408wt: 0.8770 / mu: 0.9447 (marginal change - not scored)wt: TTGCCGACAAGGTGC
mu: TTGCCAACAAGGTGC
 GCCG|acaa
Donor increased18412wt: 0.31 / mu: 0.56wt: CGACAAGGTGCAGCT
mu: CAACAAGGTGCAGCT
 ACAA|ggtg
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      681GKTDYGLMVFADKRFARGDKRGKL
mutated  all conserved    681GKTDYGLMVFANKRFARGDKRGK
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  681GKTDYGLMIFADKRYARADKRGK
Drerio  all identical  ENSDARG00000021985  681GKTDYGLMIFADKRYARADKRGK
Dmelanogaster  all identical  FBgn0261850  681GKTDYGIMIFADKRFSRHDKRSR
Celegans  no alignment  Y50D7A.11  n/a
Xtropicalis  all identical  ENSXETG00000018229  680GKTDYGIMLFADKRYARSDKRGK
protein features
start (aa)end (aa)featuredetails 
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 2041
cDNA position
(for ins/del: last normal base / first normal base)
2119
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
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 VHHYGRAVIM FGVPYVYTQS RILKARLEYL RDQFQIREND FLTFDAMRHA
AQCVGRAIRG KTDYGLMVFA NKRFARGDKR GKLPRWIQEH LTDANLNLTV DEGVQVAKYF
LRQMAQPFHR EDQLGLSLLS LEQLESEETL KRIEQIAQQL *
speed 1.90 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
back to results table
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 marginally increased18408wt: 0.8770 / mu: 0.9447 (marginal change - not scored)wt: TTGCCGACAAGGTGC
mu: TTGCCAACAAGGTGC
 GCCG|acaa
Donor increased18412wt: 0.31 / mu: 0.56wt: CGACAAGGTGCAGCT
mu: CAACAAGGTGCAGCT
 ACAA|ggtg
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 1.95 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
back to results table

Problems