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 5 transcript(s)...
Querying Taster for transcript #1: ENST00000391945
Querying Taster for transcript #2: ENST00000485403
Querying Taster for transcript #3: ENST00000391944
Querying Taster for transcript #4: ENST00000391940
Querying Taster for transcript #5: ENST00000221481
MT speed 0 s - this script 6.285442 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ERCC2disease_causing_automatic0.999999980443672simple_aaeaffected0R112Hsingle base exchangers121913020show file
ERCC2disease_causing_automatic0.999999998067059simple_aaeaffected0R112Hsingle base exchangers121913020show file
ERCC2disease_causing_automatic0.999999998067059simple_aaeaffected0R88Hsingle base exchangers121913020show file
ERCC2disease_causing_automatic0.999999998067059simple_aaeaffected0R88Hsingle base exchangers121913020show file
ERCC2disease_causing_automatic0.999999998067059simple_aaeaffected0R112Hsingle base exchangers121913020show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999980443672 (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 ENST00000391944
Genbank transcript ID N/A
UniProt peptide P18074
alteration type single base exchange
alteration region CDS
DNA changes c.335G>A
cDNA.363G>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 increased2265wt: 0.21 / mu: 0.28wt: TCCCGCAAAAACTTG
mu: TCCCACAAAAACTTG		 CCGC|aaaa
Donor increased2264wt: 0.28 / mu: 0.46wt: CTCCCGCAAAAACTT
mu: CTCCCACAAAAACTT		 CCCG|caaa
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      112KLPFLGLALSSRKNLCIHPEILHA
mutated  not conserved    112KLPFLGLALSSHKNLCIHPE
Ptroglodytes  all identical  ENSPTRG00000011149  186ALGRRQGWCPYFLARYSILH
Mmulatta  all identical  ENSMMUG00000014419  185ALGRRQGWCPYFLARYSILH
Fcatus  all identical  ENSFCAG00000002679  124KLPFLGLALSSRKNLCIHPE
Mmusculus  all identical  ENSMUSG00000030400  186ALGQRQGWCPYFLARYSILH
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 conserved  ENSXETG00000018229  187LGRQKGWCPYYLARH
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 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 335
cDNA position
(for ins/del: last normal base / first normal base)		 363
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
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 SHKNLCIHPE
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*
speed 1.32 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: 0.999999998067059 (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 increased2265wt: 0.21 / mu: 0.28wt: TCCCGCAAAAACTTG
mu: TCCCACAAAAACTTG		 CCGC|aaaa
Donor increased2264wt: 0.28 / mu: 0.46wt: CTCCCGCAAAAACTT
mu: CTCCCACAAAAACTT		 CCCG|caaa
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 1.34 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: 0.999999998067059 (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 ENST00000485403
Genbank transcript ID N/A
UniProt peptide P18074
alteration type single base exchange
alteration region CDS
DNA changes c.263G>A
cDNA.482G>A
g.2264G>A
AA changes R88H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 88
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 increased2265wt: 0.21 / mu: 0.28wt: TCCCGCAAAAACTTG
mu: TCCCACAAAAACTTG		 CCGC|aaaa
Donor increased2264wt: 0.28 / mu: 0.46wt: CTCCCGCAAAAACTT
mu: CTCCCACAAAAACTT		 CCCG|caaa
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      88KLPFLGLALSSRKNLCIHPEVTPL
mutated  not conserved    88KLPFLGLALSSHKNLCIHPEVTP
Ptroglodytes  all identical  ENSPTRG00000011149  112KLPFLGLALSSRKNLCIHPEVTP
Mmulatta  all identical  ENSMMUG00000014419  111KLPFLGLALSSRKNLCIHPEVTP
Fcatus  all identical  ENSFCAG00000002679  124KLPFLGLALSSRKNLCIHPE
Mmusculus  all identical  ENSMUSG00000030400  112KLPFLGLALSSRKNLCIHPEVTP
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000007303  112SNNFLALALSSRKNLCIHPEVSA
Drerio  all identical  ENSDARG00000021985  112KNDFLALALSSRKNLCIHPEVSS
Dmelanogaster  all identical  FBgn0261850  112PPPFTGLVLSSRKNMCIHPEVSK
Celegans  all identical  Y50D7A.11  112PVAKITVAMSARKNLCVNEPVAA
Xtropicalis  all identical  ENSXETG00000018229  113TLNFMALALSSRRNLCVNPEVSA
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 1218 / 1218
position (AA) of stopcodon in wt / mu AA sequence 406 / 406
position of stopcodon in wt / mu cDNA 1437 / 1437
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 220 / 220
chromosome 19
strand -1
last intron/exon boundary 1385
theoretical NMD boundary in CDS 1115
length of CDS 1218
coding sequence (CDS) position 263
cDNA position
(for ins/del: last normal base / first normal base)		 482
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 MRELKRTLDA KGHGVLEMPS GTGKTVSLLA LIMAYQRAYP LEVTKLIYCS RTVPEIEKVI
EELRKLLNFY EKQEGEKLPF LGLALSSRKN LCIHPEVTPL RFGKDVDGKC HSLTASYVRA
QYQHDTSLPH CRFYEEFDAH GREVPLPAGI YNLDDLKALG RRQGWCPYFL ARYSILHANV
VVYSYHYLLD PKIADLVSKE LARKAVVVFD EAHNIDNVCI DSMSVNLTRR TLDRCQGNLE
TLQKTVLRIK ETDEQRLRDE YRRLVEGLRE ASAARETDAH LANPVLPDEV LQEAVPGSIR
TAEHFLGFLR RLLEYVKWRL RVQHVVQESP PAFLSGLAQR VCIQRKPLRF CAERLRSLLH
TLEITDLADF SPLTLLANFA TLVSTYAKGQ AQHCGSSRNQ KRSHP*
mutated AA sequence MRELKRTLDA KGHGVLEMPS GTGKTVSLLA LIMAYQRAYP LEVTKLIYCS RTVPEIEKVI
EELRKLLNFY EKQEGEKLPF LGLALSSHKN LCIHPEVTPL RFGKDVDGKC HSLTASYVRA
QYQHDTSLPH CRFYEEFDAH GREVPLPAGI YNLDDLKALG RRQGWCPYFL ARYSILHANV
VVYSYHYLLD PKIADLVSKE LARKAVVVFD EAHNIDNVCI DSMSVNLTRR TLDRCQGNLE
TLQKTVLRIK ETDEQRLRDE YRRLVEGLRE ASAARETDAH LANPVLPDEV LQEAVPGSIR
TAEHFLGFLR RLLEYVKWRL RVQHVVQESP PAFLSGLAQR VCIQRKPLRF CAERLRSLLH
TLEITDLADF SPLTLLANFA TLVSTYAKGQ AQHCGSSRNQ KRSHP*
speed 1.38 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: 0.999999998067059 (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 ENST00000391940
Genbank transcript ID N/A
UniProt peptide P18074
alteration type single base exchange
alteration region CDS
DNA changes c.263G>A
cDNA.345G>A
g.2264G>A
AA changes R88H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 88
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 increased2265wt: 0.21 / mu: 0.28wt: TCCCGCAAAAACTTG
mu: TCCCACAAAAACTTG		 CCGC|aaaa
Donor increased2264wt: 0.28 / mu: 0.46wt: CTCCCGCAAAAACTT
mu: CTCCCACAAAAACTT		 CCCG|caaa
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      88KLPFLGLALSSRKNLCIHPEVTPL
mutated  not conserved    88KLPFLGLALSSHKNLCIHPEVTP
Ptroglodytes  all identical  ENSPTRG00000011149  112KLPFLGLALSSRKNLCIHPEVTP
Mmulatta  all identical  ENSMMUG00000014419  111KLPFLGLALSSRKNLCIHPEVTP
Fcatus  all identical  ENSFCAG00000002679  124KLPFLGLALSSRKNLCIHPE
Mmusculus  all identical  ENSMUSG00000030400  112KLPFLGLALSSRKNLCIHPEVTP
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000007303  112SNNFLALALSSRKNLCIHPEVSA
Drerio  all identical  ENSDARG00000021985  112KNDFLALALSSRKNLCIHPEVSS
Dmelanogaster  all identical  FBgn0261850  112PPPFTGLVLSSRKNMCIHPEVSK
Celegans  all identical  Y50D7A.11  112PVAKITVAMSARKNLCVNEPVAA
Xtropicalis  all identical  ENSXETG00000018229  113TLNFMALALSSRRNLCVNPEVSA
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 1218 / 1218
position (AA) of stopcodon in wt / mu AA sequence 406 / 406
position of stopcodon in wt / mu cDNA 1300 / 1300
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 83 / 83
chromosome 19
strand -1
last intron/exon boundary 1248
theoretical NMD boundary in CDS 1115
length of CDS 1218
coding sequence (CDS) position 263
cDNA position
(for ins/del: last normal base / first normal base)		 345
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 MRELKRTLDA KGHGVLEMPS GTGKTVSLLA LIMAYQRAYP LEVTKLIYCS RTVPEIEKVI
EELRKLLNFY EKQEGEKLPF LGLALSSRKN LCIHPEVTPL RFGKDVDGKC HSLTASYVRA
QYQHDTSLPH CRFYEEFDAH GREVPLPAGI YNLDDLKALG RRQGWCPYFL ARYSILHANV
VVYSYHYLLD PKIADLVSKE LARKAVVVFD EAHNIDNVCI DSMSVNLTRR TLDRCQGNLE
TLQKTVLRIK ETDEQRLRDE YRRLVEGLRE ASAARETDAH LANPVLPDEV LQEAVPGSIR
TAEHFLGFLR RLLEYVKWRL RVQHVVQESP PAFLSGLAQR VCIQRKPLRF CAERLRSLLH
TLEITDLADF SPLTLLANFA TLVSTYAKGQ AQHCGSSRNQ KRSHP*
mutated AA sequence MRELKRTLDA KGHGVLEMPS GTGKTVSLLA LIMAYQRAYP LEVTKLIYCS RTVPEIEKVI
EELRKLLNFY EKQEGEKLPF LGLALSSHKN LCIHPEVTPL RFGKDVDGKC HSLTASYVRA
QYQHDTSLPH CRFYEEFDAH GREVPLPAGI YNLDDLKALG RRQGWCPYFL ARYSILHANV
VVYSYHYLLD PKIADLVSKE LARKAVVVFD EAHNIDNVCI DSMSVNLTRR TLDRCQGNLE
TLQKTVLRIK ETDEQRLRDE YRRLVEGLRE ASAARETDAH LANPVLPDEV LQEAVPGSIR
TAEHFLGFLR RLLEYVKWRL RVQHVVQESP PAFLSGLAQR VCIQRKPLRF CAERLRSLLH
TLEITDLADF SPLTLLANFA TLVSTYAKGQ AQHCGSSRNQ KRSHP*
speed 1.30 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: 0.999999998067059 (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 ENST00000221481
Genbank transcript ID N/A
UniProt peptide P18074
alteration type single base exchange
alteration region CDS
DNA changes c.335G>A
cDNA.352G>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 increased2265wt: 0.21 / mu: 0.28wt: TCCCGCAAAAACTTG
mu: TCCCACAAAAACTTG		 CCGC|aaaa
Donor increased2264wt: 0.28 / mu: 0.46wt: CTCCCGCAAAAACTT
mu: CTCCCACAAAAACTT		 CCCG|caaa
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      112KLPFLGLALSSRKNLCIHPETTSA
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  112PVAKITVAMSARKNLCVN
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 384 / 384
position (AA) of stopcodon in wt / mu AA sequence 128 / 128
position of stopcodon in wt / mu cDNA 401 / 401
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 18 / 18
chromosome 19
strand -1
last intron/exon boundary 609
theoretical NMD boundary in CDS 541
length of CDS 384
coding sequence (CDS) position 335
cDNA position
(for ins/del: last normal base / first normal base)		 352
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
TTSASTP*
mutated AA sequence MKLNVDGLLV YFPYDYIYPE QFSYMRELKR TLDAKGHGVL EMPSGTGKTV SLLALIMAYQ
RAYPLEVTKL IYCSRTVPEI EKVIEELRKL LNFYEKQEGE KLPFLGLALS SHKNLCIHPE
TTSASTP*
speed 1.42 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