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MutationTaster - study a chromosomal position

MTQE documentation
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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000366794
MT speed 1.25 s - this script 5.056675 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
PARP1polymorphism_automatic0.999999999869817simple_aaeaffectedV762Asingle base exchangers1136410show file

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Prediction

polymorphism

Model: simple_aae, prob: 1.30182899293225e-10 (classification due to TGP/ExAC, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • homozygous in TGP or ExAC
  • known disease mutation at this position (HGMD CM042761)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:226555302A>GN/A show variant in all transcripts   IGV
HGNC symbol PARP1
Ensembl transcript ID ENST00000366794
Genbank transcript ID NM_001618
UniProt peptide P09874
alteration type single base exchange
alteration region CDS
DNA changes c.2285T>C
cDNA.2429T>C
g.40479T>C
AA changes V762A Score: 64 explain score(s)
position(s) of altered AA
if AA alteration in CDS
762
frameshift no
known variant Reference ID: rs1136410
databasehomozygous (G/G)heterozygousallele carriers
1000G184618802
ExAC33991768321082

known disease mutation at this position, please check HGMD for details (HGMD ID CM042761)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.1110.995
5.0531
(flanking)6.1181
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 increased40471wt: 0.9886 / mu: 0.9888 (marginal change - not scored)wt: GGCTTTCTTTTGCTCCTCCAGGCCAAGGTGGAAATGCTTGA
mu: GGCTTTCTTTTGCTCCTCCAGGCCAAGGCGGAAATGCTTGA
 ccag|GCCA
Acc marginally increased40476wt: 0.2770 / mu: 0.3487 (marginal change - not scored)wt: TCTTTTGCTCCTCCAGGCCAAGGTGGAAATGCTTGACAACC
mu: TCTTTTGCTCCTCCAGGCCAAGGCGGAAATGCTTGACAACC
 ccaa|GGTG
Acc marginally increased40472wt: 0.2770 / mu: 0.3482 (marginal change - not scored)wt: GCTTTCTTTTGCTCCTCCAGGCCAAGGTGGAAATGCTTGAC
mu: GCTTTCTTTTGCTCCTCCAGGCCAAGGCGGAAATGCTTGAC
 cagg|CCAA
Donor increased40479wt: 0.43 / mu: 0.56wt: CAAGGTGGAAATGCT
mu: CAAGGCGGAAATGCT
 AGGT|ggaa
Donor marginally increased40471wt: 0.9976 / mu: 0.9981 (marginal change - not scored)wt: CTCCAGGCCAAGGTG
mu: CTCCAGGCCAAGGCG
 CCAG|gcca
Donor increased40480wt: 0.39 / mu: 0.86wt: AAGGTGGAAATGCTT
mu: AAGGCGGAAATGCTT
 GGTG|gaaa
Donor increased40478wt: 0.65 / mu: 0.82wt: CCAAGGTGGAAATGC
mu: CCAAGGCGGAAATGC
 AAGG|tgga
distance from splice site 8
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      762LLNNADSVQAKVEMLDNLLDIEVA
mutated  not conserved    762LLNNADSVQAKAEMLDNLLDIEV
Ptroglodytes  all identical  ENSPTRG00000002049  762VLNNADSVQAKVEMLDNLLDIEV
Mmulatta  all identical  ENSMMUG00000021820  762LLNSADSVQAKVEMLDNLLDIEV
Fcatus  all identical  ENSFCAG00000005777  761XXAKVEMLDNLLDIEV
Mmusculus  all identical  ENSMUSG00000026496  762LLNNADSVQAKVEMLDNLLDIEV
Ggallus  all identical  ENSGALG00000009228  763LLSNLEYIQAKVQMLDNLL
Trubripes  all identical  ENSTRUG00000014490  762LLNNLNYIQAKVQMLDNLLDIEV
Drerio  all identical  ENSDARG00000019529  761LLSNVDYIQQKVQMLDNLLDIE
Dmelanogaster  not conserved  FBgn0010247  744LIETHQQIEDLRQMLDSLAEI
Celegans  not conserved  Y71F9AL.18  686PIDSFHKIKEKNNMLNALLDIKF
Xtropicalis  all identical  ENSXETG00000022610  744LLNNLEYIQAKVQMLDNLLDIEV
protein features
start (aa)end (aa)featuredetails 
662779DOMAINPARP alpha-helical.lost
755777HELIXlost
778781TURNmight get lost (downstream of altered splice site)
782782MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
785787STRANDmight get lost (downstream of altered splice site)
7881014DOMAINPARP catalytic.might get lost (downstream of altered splice site)
789796HELIXmight get lost (downstream of altered splice site)
797797MUTAGENL->P: 1.5% of wild-type activity.might get lost (downstream of altered splice site)
799803STRANDmight get lost (downstream of altered splice site)
806808STRANDmight get lost (downstream of altered splice site)
809820HELIXmight get lost (downstream of altered splice site)
824826STRANDmight get lost (downstream of altered splice site)
827827CONFLICTN -> S (in Ref. 3; AAA60155).might get lost (downstream of altered splice site)
828841STRANDmight get lost (downstream of altered splice site)
842850TURNmight get lost (downstream of altered splice site)
851853HELIXmight get lost (downstream of altered splice site)
857864STRANDmight get lost (downstream of altered splice site)
866868HELIXmight get lost (downstream of altered splice site)
868868MUTAGENN->S: 4% of wild-type activity.might get lost (downstream of altered splice site)
869875HELIXmight get lost (downstream of altered splice site)
882884STRANDmight get lost (downstream of altered splice site)
886888HELIXmight get lost (downstream of altered splice site)
889891STRANDmight get lost (downstream of altered splice site)
890890MUTAGENM->V: <0.5% of wild-type activity.might get lost (downstream of altered splice site)
892900STRANDmight get lost (downstream of altered splice site)
893893MUTAGENK->I: Abolishes enzymatic activity.might get lost (downstream of altered splice site)
897897MUTAGENF->S: 10% of wild-type activity.might get lost (downstream of altered splice site)
899899MUTAGEND->N: 0.6% of wild-type activity.might get lost (downstream of altered splice site)
901905HELIXmight get lost (downstream of altered splice site)
906908HELIXmight get lost (downstream of altered splice site)
908908MUTAGENC->R: <0.5% of wild-type activity.might get lost (downstream of altered splice site)
908908CONFLICTC -> Y (in Ref. 3; AAA60155).might get lost (downstream of altered splice site)
912914STRANDmight get lost (downstream of altered splice site)
916925STRANDmight get lost (downstream of altered splice site)
926926MUTAGENL->F: 1.5% of wild-type activity.might get lost (downstream of altered splice site)
928934STRANDmight get lost (downstream of altered splice site)
947950STRANDmight get lost (downstream of altered splice site)
953956STRANDmight get lost (downstream of altered splice site)
958960HELIXmight get lost (downstream of altered splice site)
962964STRANDmight get lost (downstream of altered splice site)
967969STRANDmight get lost (downstream of altered splice site)
974976STRANDmight get lost (downstream of altered splice site)
980980CONFLICTN -> I (in Ref. 3; AAA60155).might get lost (downstream of altered splice site)
981986STRANDmight get lost (downstream of altered splice site)
986986MUTAGENY->H: 14% of wild-type activity and increased branching 15-fold.might get lost (downstream of altered splice site)
988988MUTAGENE->K: 1.25% of wild-type activity; only monomers are added.might get lost (downstream of altered splice site)
988992STRANDmight get lost (downstream of altered splice site)
994996HELIXmight get lost (downstream of altered splice site)
9971009STRANDmight get lost (downstream of altered splice site)
10031003MUTAGENL->P: 1.5% of wild-type activity.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3045 / 3045
position (AA) of stopcodon in wt / mu AA sequence 1015 / 1015
position of stopcodon in wt / mu cDNA 3189 / 3189
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 145 / 145
chromosome 1
strand -1
last intron/exon boundary 3108
theoretical NMD boundary in CDS 2913
length of CDS 3045
coding sequence (CDS) position 2285
cDNA position
(for ins/del: last normal base / first normal base)
2429
gDNA position
(for ins/del: last normal base / first normal base)
40479
chromosomal position
(for ins/del: last normal base / first normal base)
226555302
original gDNA sequence snippet TTTGCTCCTCCAGGCCAAGGTGGAAATGCTTGACAACCTGC
altered gDNA sequence snippet TTTGCTCCTCCAGGCCAAGGCGGAAATGCTTGACAACCTGC
original cDNA sequence snippet AGACAGTGTGCAGGCCAAGGTGGAAATGCTTGACAACCTGC
altered cDNA sequence snippet AGACAGTGTGCAGGCCAAGGCGGAAATGCTTGACAACCTGC
wildtype AA sequence MAESSDKLYR VEYAKSGRAS CKKCSESIPK DSLRMAIMVQ SPMFDGKVPH WYHFSCFWKV
GHSIRHPDVE VDGFSELRWD DQQKVKKTAE AGGVTGKGQD GIGSKAEKTL GDFAAEYAKS
NRSTCKGCME KIEKGQVRLS KKMVDPEKPQ LGMIDRWYHP GCFVKNREEL GFRPEYSASQ
LKGFSLLATE DKEALKKQLP GVKSEGKRKG DEVDGVDEVA KKKSKKEKDK DSKLEKALKA
QNDLIWNIKD ELKKVCSTND LKELLIFNKQ QVPSGESAIL DRVADGMVFG ALLPCEECSG
QLVFKSDAYY CTGDVTAWTK CMVKTQTPNR KEWVTPKEFR EISYLKKLKV KKQDRIFPPE
TSASVAATPP PSTASAPAAV NSSASADKPL SNMKILTLGK LSRNKDEVKA MIEKLGGKLT
GTANKASLCI STKKEVEKMN KKMEEVKEAN IRVVSEDFLQ DVSASTKSLQ ELFLAHILSP
WGAEVKAEPV EVVAPRGKSG AALSKKSKGQ VKEEGINKSE KRMKLTLKGG AAVDPDSGLE
HSAHVLEKGG KVFSATLGLV DIVKGTNSYY KLQLLEDDKE NRYWIFRSWG RVGTVIGSNK
LEQMPSKEDA IEHFMKLYEE KTGNAWHSKN FTKYPKKFYP LEIDYGQDEE AVKKLTVNPG
TKSKLPKPVQ DLIKMIFDVE SMKKAMVEYE IDLQKMPLGK LSKRQIQAAY SILSEVQQAV
SQGSSDSQIL DLSNRFYTLI PHDFGMKKPP LLNNADSVQA KVEMLDNLLD IEVAYSLLRG
GSDDSSKDPI DVNYEKLKTD IKVVDRDSEE AEIIRKYVKN THATTHNAYD LEVIDIFKIE
REGECQRYKP FKQLHNRRLL WHGSRTTNFA GILSQGLRIA PPEAPVTGYM FGKGIYFADM
VSKSANYCHT SQGDPIGLIL LGEVALGNMY ELKHASHISK LPKGKHSVKG LGKTTPDPSA
NISLDGVDVP LGTGISSGVN DTSLLYNEYI VYDIAQVNLK YLLKLKFNFK TSLW*
mutated AA sequence MAESSDKLYR VEYAKSGRAS CKKCSESIPK DSLRMAIMVQ SPMFDGKVPH WYHFSCFWKV
GHSIRHPDVE VDGFSELRWD DQQKVKKTAE AGGVTGKGQD GIGSKAEKTL GDFAAEYAKS
NRSTCKGCME KIEKGQVRLS KKMVDPEKPQ LGMIDRWYHP GCFVKNREEL GFRPEYSASQ
LKGFSLLATE DKEALKKQLP GVKSEGKRKG DEVDGVDEVA KKKSKKEKDK DSKLEKALKA
QNDLIWNIKD ELKKVCSTND LKELLIFNKQ QVPSGESAIL DRVADGMVFG ALLPCEECSG
QLVFKSDAYY CTGDVTAWTK CMVKTQTPNR KEWVTPKEFR EISYLKKLKV KKQDRIFPPE
TSASVAATPP PSTASAPAAV NSSASADKPL SNMKILTLGK LSRNKDEVKA MIEKLGGKLT
GTANKASLCI STKKEVEKMN KKMEEVKEAN IRVVSEDFLQ DVSASTKSLQ ELFLAHILSP
WGAEVKAEPV EVVAPRGKSG AALSKKSKGQ VKEEGINKSE KRMKLTLKGG AAVDPDSGLE
HSAHVLEKGG KVFSATLGLV DIVKGTNSYY KLQLLEDDKE NRYWIFRSWG RVGTVIGSNK
LEQMPSKEDA IEHFMKLYEE KTGNAWHSKN FTKYPKKFYP LEIDYGQDEE AVKKLTVNPG
TKSKLPKPVQ DLIKMIFDVE SMKKAMVEYE IDLQKMPLGK LSKRQIQAAY SILSEVQQAV
SQGSSDSQIL DLSNRFYTLI PHDFGMKKPP LLNNADSVQA KAEMLDNLLD IEVAYSLLRG
GSDDSSKDPI DVNYEKLKTD IKVVDRDSEE AEIIRKYVKN THATTHNAYD LEVIDIFKIE
REGECQRYKP FKQLHNRRLL WHGSRTTNFA GILSQGLRIA PPEAPVTGYM FGKGIYFADM
VSKSANYCHT SQGDPIGLIL LGEVALGNMY ELKHASHISK LPKGKHSVKG LGKTTPDPSA
NISLDGVDVP LGTGISSGVN DTSLLYNEYI VYDIAQVNLK YLLKLKFNFK TSLW*
speed 1.25 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
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