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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: ENST00000360971
MT speed 0 s - this script 2.83492 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ENPP1disease_causing_automatic0.999999999999999simple_aaeaffected0G266Vsingle base exchangers121908248show file

Taster files

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mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999999999 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM101021)
  • known disease mutation: rs13594 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:132181528G>TN/A show variant in all transcripts   IGV
HGNC symbol ENPP1
Ensembl transcript ID ENST00000360971
Genbank transcript ID NM_006208
UniProt peptide P22413
alteration type single base exchange
alteration region CDS
DNA changes c.797G>T
cDNA.817G>T
g.52373G>T
AA changes G266V Score: 109 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 266
frameshift no
known variant Reference ID: rs121908248
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs13594 (pathogenic for Arterial calcification, generalized, of infancy, 1|Hypophosphatemic rickets, autosomal recessive, 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM101021)

known disease mutation at this position, please check HGMD for details (HGMD ID CM101021)
known disease mutation at this position, please check HGMD for details (HGMD ID CM101021)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.931
5.5451
(flanking)-2.1480.111
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost52371sequence motif lost- wt: ttag|GGAT
 mu: ttag.GTAT
Acc marginally increased52364wt: 0.9033 / mu: 0.9095 (marginal change - not scored)wt: TGCATATAATCTGTTTTATCTTTTTTAGGGATTGTATCCAG
mu: TGCATATAATCTGTTTTATCTTTTTTAGGTATTGTATCCAG		 atct|TTTT
Acc marginally increased52373wt: 0.2079 / mu: 0.2318 (marginal change - not scored)wt: TCTGTTTTATCTTTTTTAGGGATTGTATCCAGAATCTCATG
mu: TCTGTTTTATCTTTTTTAGGTATTGTATCCAGAATCTCATG		 aggg|ATTG
Acc increased52382wt: 0.24 / mu: 0.55wt: TCTTTTTTAGGGATTGTATCCAGAATCTCATGGCATAATCG
mu: TCTTTTTTAGGTATTGTATCCAGAATCTCATGGCATAATCG		 atcc|AGAA
Acc gained523770.57mu: TTTTATCTTTTTTAGGTATTGTATCCAGAATCTCATGGCAT attg|TATC
Acc gained523780.79mu: TTTATCTTTTTTAGGTATTGTATCCAGAATCTCATGGCATA ttgt|ATCC
Acc gained523830.44mu: CTTTTTTAGGTATTGTATCCAGAATCTCATGGCATAATCGA tcca|GAAT
Acc gained523750.55mu: TGTTTTATCTTTTTTAGGTATTGTATCCAGAATCTCATGGC gtat|TGTA
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      266KTFPNHYSIVTGLYPESHGIIDNK
mutated  not conserved    266KTFPNHYSIVTVLYPESHGIIDN
Ptroglodytes  all identical  ENSPTRG00000018603  266KTFPNHYSIVTGLYPESHGIIDN
Mmulatta  all identical  ENSMMUG00000014151  266KTFPNHYSIVTGLYPESHGIIDN
Fcatus  all identical  ENSFCAG00000014133  207XXXXXXXXXXXGLYPESHGIIDN
Mmusculus  all identical  ENSMUSG00000037370  248KTFPNHYSIVTGLYPESHGIIDN
Ggallus  all identical  ENSGALG00000002896  263KTFPNHYSIVTGLYPESHGIIDN
Trubripes  all identical  ENSTRUG00000017715  81KTFPNHYTIVTGLYPESHGIVDN
Drerio  all identical  ENSDARG00000005789  233KTFPNHYTIVTGLYPETHGIVDN
Dmelanogaster  no homologue    
Celegans  all identical  C27A7.3  133KTFPNHYTMVTGLYPESHGITDN
Xtropicalis  all identical  ENSXETG00000030043  163KTFPNHYSIVTGLYPESHGLVDN
protein features
start (aa)end (aa)featuredetails 
98925TOPO_DOMExtracellular (Potential).lost
191591REGIONPhosphodiesterase.lost
285285CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
341341CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
376376METALDivalent metal cation 1 (Probable).might get lost (downstream of altered splice site)
380380METALDivalent metal cation 1 (Probable).might get lost (downstream of altered splice site)
423423METALDivalent metal cation 2 (Probable).might get lost (downstream of altered splice site)
424424METALDivalent metal cation 2 (Probable).might get lost (downstream of altered splice site)
477477CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
480480DISULFIDBy similarity.might get lost (downstream of altered splice site)
535535METALDivalent metal cation 1 (Probable).might get lost (downstream of altered splice site)
585585CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
643643CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
654925REGIONNuclease.might get lost (downstream of altered splice site)
700700CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
731731CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
748748CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
868868DISULFIDBy similarity.might get lost (downstream of altered splice site)
915915SITEEssential for catalytic activity (By similarity).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 2778 / 2778
position (AA) of stopcodon in wt / mu AA sequence 926 / 926
position of stopcodon in wt / mu cDNA 2798 / 2798
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 21 / 21
chromosome 6
strand 1
last intron/exon boundary 2628
theoretical NMD boundary in CDS 2557
length of CDS 2778
coding sequence (CDS) position 797
cDNA position
(for ins/del: last normal base / first normal base)		 817
gDNA position
(for ins/del: last normal base / first normal base)		 52373
chromosomal position
(for ins/del: last normal base / first normal base)		 132181528
original gDNA sequence snippet TCTGTTTTATCTTTTTTAGGGATTGTATCCAGAATCTCATG
altered gDNA sequence snippet TCTGTTTTATCTTTTTTAGGTATTGTATCCAGAATCTCATG
original cDNA sequence snippet TCACTACAGCATTGTCACCGGATTGTATCCAGAATCTCATG
altered cDNA sequence snippet TCACTACAGCATTGTCACCGTATTGTATCCAGAATCTCATG
wildtype AA sequence MERDGCAGGG SRGGEGGRAP REGPAGNGRD RGRSHAAEAP GDPQAAASLL APMDVGEEPL
EKAARARTAK DPNTYKVLSL VLSVCVLTTI LGCIFGLKPS CAKEVKSCKG RCFERTFGNC
RCDAACVELG NCCLDYQETC IEPEHIWTCN KFRCGEKRLT RSLCACSDDC KDKGDCCINY
SSVCQGEKSW VEEPCESINE PQCPAGFETP PTLLFSLDGF RAEYLHTWGG LLPVISKLKK
CGTYTKNMRP VYPTKTFPNH YSIVTGLYPE SHGIIDNKMY DPKMNASFSL KSKEKFNPEW
YKGEPIWVTA KYQGLKSGTF FWPGSDVEIN GIFPDIYKMY NGSVPFEERI LAVLQWLQLP
KDERPHFYTL YLEEPDSSGH SYGPVSSEVI KALQRVDGMV GMLMDGLKEL NLHRCLNLIL
ISDHGMEQGS CKKYIYLNKY LGDVKNIKVI YGPAARLRPS DVPDKYYSFN YEGIARNLSC
REPNQHFKPY LKHFLPKRLH FAKSDRIEPL TFYLDPQWQL ALNPSERKYC GSGFHGSDNV
FSNMQALFVG YGPGFKHGIE ADTFENIEVY NLMCDLLNLT PAPNNGTHGS LNHLLKNPVY
TPKHPKEVHP LVQCPFTRNP RDNLGCSCNP SILPIEDFQT QFNLTVAEEK IIKHETLPYG
RPRVLQKENT ICLLSQHQFM SGYSQDILMP LWTSYTVDRN DSFSTEDFSN CLYQDFRIPL
SPVHKCSFYK NNTKVSYGFL SPPQLNKNSS GIYSEALLTT NIVPMYQSFQ VIWRYFHDTL
LRKYAEERNG VNVVSGPVFD FDYDGRCDSL ENLRQKRRVI RNQEILIPTH FFIVLTSCKD
TSQTPLHCEN LDTLAFILPH RTDNSESCVH GKHDSSWVEE LLMLHRARIT DVEHITGLSF
YQQRKEPVSD ILKLKTHLPT FSQED*
mutated AA sequence MERDGCAGGG SRGGEGGRAP REGPAGNGRD RGRSHAAEAP GDPQAAASLL APMDVGEEPL
EKAARARTAK DPNTYKVLSL VLSVCVLTTI LGCIFGLKPS CAKEVKSCKG RCFERTFGNC
RCDAACVELG NCCLDYQETC IEPEHIWTCN KFRCGEKRLT RSLCACSDDC KDKGDCCINY
SSVCQGEKSW VEEPCESINE PQCPAGFETP PTLLFSLDGF RAEYLHTWGG LLPVISKLKK
CGTYTKNMRP VYPTKTFPNH YSIVTVLYPE SHGIIDNKMY DPKMNASFSL KSKEKFNPEW
YKGEPIWVTA KYQGLKSGTF FWPGSDVEIN GIFPDIYKMY NGSVPFEERI LAVLQWLQLP
KDERPHFYTL YLEEPDSSGH SYGPVSSEVI KALQRVDGMV GMLMDGLKEL NLHRCLNLIL
ISDHGMEQGS CKKYIYLNKY LGDVKNIKVI YGPAARLRPS DVPDKYYSFN YEGIARNLSC
REPNQHFKPY LKHFLPKRLH FAKSDRIEPL TFYLDPQWQL ALNPSERKYC GSGFHGSDNV
FSNMQALFVG YGPGFKHGIE ADTFENIEVY NLMCDLLNLT PAPNNGTHGS LNHLLKNPVY
TPKHPKEVHP LVQCPFTRNP RDNLGCSCNP SILPIEDFQT QFNLTVAEEK IIKHETLPYG
RPRVLQKENT ICLLSQHQFM SGYSQDILMP LWTSYTVDRN DSFSTEDFSN CLYQDFRIPL
SPVHKCSFYK NNTKVSYGFL SPPQLNKNSS GIYSEALLTT NIVPMYQSFQ VIWRYFHDTL
LRKYAEERNG VNVVSGPVFD FDYDGRCDSL ENLRQKRRVI RNQEILIPTH FFIVLTSCKD
TSQTPLHCEN LDTLAFILPH RTDNSESCVH GKHDSSWVEE LLMLHRARIT DVEHITGLSF
YQQRKEPVSD ILKLKTHLPT FSQED*
speed 0.72 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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