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: ENST00000361216
Querying Taster for transcript #2: ENST00000392233
MT speed 0 s - this script 4.460784 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ATP1A2disease_causing_automatic0.999999946429366simple_aaeaffected0W887Rsingle base exchangers28933399show file
ATP1A2disease_causing_automatic0.999999946429366simple_aaeaffected0W887Rsingle base exchangers28933399show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999946429366 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM030197)
  • known disease mutation: rs12918 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:160106455T>CN/A show variant in all transcripts   IGV
HGNC symbol ATP1A2
Ensembl transcript ID ENST00000361216
Genbank transcript ID NM_000702
UniProt peptide P50993
alteration type single base exchange
alteration region CDS
DNA changes c.2659T>C
cDNA.2748T>C
g.20907T>C
AA changes W887R Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS
887
frameshift no
known variant Reference ID: rs28933399
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs12918 (pathogenic for Familial hemiplegic migraine type 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM030197)

known disease mutation at this position, please check HGMD for details (HGMD ID CM030197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM030197)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.7270.998
4.3471
(flanking)5.1731
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased20898wt: 0.20 / mu: 0.38wt: GAATCCGCCTCGACT
mu: GAATCCGCCTCGACC
 ATCC|gcct
Donor marginally increased20907wt: 0.9654 / mu: 0.9885 (marginal change - not scored)wt: TCGACTGGGATGACC
mu: TCGACCGGGATGACC
 GACT|ggga
distance from splice site 51
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      887LPSRLLGIRLDWDDRTMNDLEDSY
mutated  not conserved    887LPSRLLGIRLDRDDRTMNDLEDS
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000017833  887LPSRLLGIRLDWDDRTMNDLEDS
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000007097  887LPSRLLGIRLDWDDRTTNDLEDS
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000010472  884LPQTLLGIRLDWDDRTVNDLEDG
Dmelanogaster  all identical  FBgn0002921  908LPKKLFGIRKMWDSKAVNDLTDS
Celegans  all identical  B0365.3  863MPWDLYQLRAQWDSRAYNNVLDS
Xtropicalis  all identical  ENSXETG00000008125  883LPSRLLGIRLDWDDRSNNDVEDS
protein features
start (aa)end (aa)featuredetails 
864915TOPO_DOMExtracellular (Potential).lost
916935TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
936948TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
940940MOD_RESPhosphoserine; by PKA (By similarity).might get lost (downstream of altered splice site)
949967TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
968982TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
9831003TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
10041020TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3063 / 3063
position (AA) of stopcodon in wt / mu AA sequence 1021 / 1021
position of stopcodon in wt / mu cDNA 3152 / 3152
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 90 / 90
chromosome 1
strand 1
last intron/exon boundary 3124
theoretical NMD boundary in CDS 2984
length of CDS 3063
coding sequence (CDS) position 2659
cDNA position
(for ins/del: last normal base / first normal base)
2748
gDNA position
(for ins/del: last normal base / first normal base)
20907
chromosomal position
(for ins/del: last normal base / first normal base)
160106455
original gDNA sequence snippet TACTGGGAATCCGCCTCGACTGGGATGACCGGACCATGAAT
altered gDNA sequence snippet TACTGGGAATCCGCCTCGACCGGGATGACCGGACCATGAAT
original cDNA sequence snippet TACTGGGAATCCGCCTCGACTGGGATGACCGGACCATGAAT
altered cDNA sequence snippet TACTGGGAATCCGCCTCGACCGGGATGACCGGACCATGAAT
wildtype AA sequence MGRGAGREYS PAATTAENGG GKKKQKEKEL DELKKEVAMD DHKLSLDELG RKYQVDLSKG
LTNQRAQDVL ARDGPNALTP PPTTPEWVKF CRQLFGGFSI LLWIGAILCF LAYGIQAAME
DEPSNDNLYL GVVLAAVVIV TGCFSYYQEA KSSKIMDSFK NMVPQQALVI REGEKMQINA
EEVVVGDLVE VKGGDRVPAD LRIISSHGCK VDNSSLTGES EPQTRSPEFT HENPLETRNI
CFFSTNCVEG TARGIVIATG DRTVMGRIAT LASGLEVGRT PIAMEIEHFI QLITGVAVFL
GVSFFVLSLI LGYSWLEAVI FLIGIIVANV PEGLLATVTV CLTLTAKRMA RKNCLVKNLE
AVETLGSTST ICSDKTGTLT QNRMTVAHMW FDNQIHEADT TEDQSGATFD KRSPTWTALS
RIAGLCNRAV FKAGQENISV SKRDTAGDAS ESALLKCIEL SCGSVRKMRD RNPKVAEIPF
NSTNKYQLSI HEREDSPQSH VLVMKGAPER ILDRCSTILV QGKEIPLDKE MQDAFQNAYM
ELGGLGERVL GFCQLNLPSG KFPRGFKFDT DELNFPTEKL CFVGLMSMID PPRAAVPDAV
GKCRSAGIKV IMVTGDHPIT AKAIAKGVGI ISEGNETVED IAARLNIPMS QVNPREAKAC
VVHGSDLKDM TSEQLDEILK NHTEIVFART SPQQKLIIVE GCQRQGAIVA VTGDGVNDSP
ALKKADIGIA MGISGSDVSK QAADMILLDD NFASIVTGVE EGRLIFDNLK KSIAYTLTSN
IPEITPFLLF IIANIPLPLG TVTILCIDLG TDMVPAISLA YEAAESDIMK RQPRNSQTDK
LVNERLISMA YGQIGMIQAL GGFFTYFVIL AENGFLPSRL LGIRLDWDDR TMNDLEDSYG
QEWTYEQRKV VEFTCHTAFF ASIVVVQWAD LIICKTRRNS VFQQGMKNKI LIFGLLEETA
LAAFLSYCPG MGVALRMYPL KVTWWFCAFP YSLLIFIYDE VRKLILRRYP GGWVEKETYY
*
mutated AA sequence MGRGAGREYS PAATTAENGG GKKKQKEKEL DELKKEVAMD DHKLSLDELG RKYQVDLSKG
LTNQRAQDVL ARDGPNALTP PPTTPEWVKF CRQLFGGFSI LLWIGAILCF LAYGIQAAME
DEPSNDNLYL GVVLAAVVIV TGCFSYYQEA KSSKIMDSFK NMVPQQALVI REGEKMQINA
EEVVVGDLVE VKGGDRVPAD LRIISSHGCK VDNSSLTGES EPQTRSPEFT HENPLETRNI
CFFSTNCVEG TARGIVIATG DRTVMGRIAT LASGLEVGRT PIAMEIEHFI QLITGVAVFL
GVSFFVLSLI LGYSWLEAVI FLIGIIVANV PEGLLATVTV CLTLTAKRMA RKNCLVKNLE
AVETLGSTST ICSDKTGTLT QNRMTVAHMW FDNQIHEADT TEDQSGATFD KRSPTWTALS
RIAGLCNRAV FKAGQENISV SKRDTAGDAS ESALLKCIEL SCGSVRKMRD RNPKVAEIPF
NSTNKYQLSI HEREDSPQSH VLVMKGAPER ILDRCSTILV QGKEIPLDKE MQDAFQNAYM
ELGGLGERVL GFCQLNLPSG KFPRGFKFDT DELNFPTEKL CFVGLMSMID PPRAAVPDAV
GKCRSAGIKV IMVTGDHPIT AKAIAKGVGI ISEGNETVED IAARLNIPMS QVNPREAKAC
VVHGSDLKDM TSEQLDEILK NHTEIVFART SPQQKLIIVE GCQRQGAIVA VTGDGVNDSP
ALKKADIGIA MGISGSDVSK QAADMILLDD NFASIVTGVE EGRLIFDNLK KSIAYTLTSN
IPEITPFLLF IIANIPLPLG TVTILCIDLG TDMVPAISLA YEAAESDIMK RQPRNSQTDK
LVNERLISMA YGQIGMIQAL GGFFTYFVIL AENGFLPSRL LGIRLDRDDR TMNDLEDSYG
QEWTYEQRKV VEFTCHTAFF ASIVVVQWAD LIICKTRRNS VFQQGMKNKI LIFGLLEETA
LAAFLSYCPG MGVALRMYPL KVTWWFCAFP YSLLIFIYDE VRKLILRRYP GGWVEKETYY
*
speed 1.26 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: 0.999999946429366 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM030197)
  • known disease mutation: rs12918 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:160106455T>CN/A show variant in all transcripts   IGV
HGNC symbol ATP1A2
Ensembl transcript ID ENST00000392233
Genbank transcript ID N/A
UniProt peptide P50993
alteration type single base exchange
alteration region CDS
DNA changes c.2659T>C
cDNA.2744T>C
g.20907T>C
AA changes W887R Score: 101 explain score(s)
position(s) of altered AA
if AA alteration in CDS
887
frameshift no
known variant Reference ID: rs28933399
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs12918 (pathogenic for Familial hemiplegic migraine type 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM030197)

known disease mutation at this position, please check HGMD for details (HGMD ID CM030197)
known disease mutation at this position, please check HGMD for details (HGMD ID CM030197)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.7270.998
4.3471
(flanking)5.1731
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased20898wt: 0.20 / mu: 0.38wt: GAATCCGCCTCGACT
mu: GAATCCGCCTCGACC
 ATCC|gcct
Donor marginally increased20907wt: 0.9654 / mu: 0.9885 (marginal change - not scored)wt: TCGACTGGGATGACC
mu: TCGACCGGGATGACC
 GACT|ggga
distance from splice site 51
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      887LPSRLLGIRLDWDDRTMNDLEDSY
mutated  not conserved    887LPSRLLGIRLDRDDRTMNDLEDS
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000017833  887LPSRLLGIRLDWDDRTMNDLEDS
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000007097  887LPSRLLGIRLDWDDRTTNDLEDS
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000010472  884LPQTLLGIRLDWDDRTVNDLEDG
Dmelanogaster  all identical  FBgn0002921  908LPKKLFGIRKMWDSKAVNDLTDS
Celegans  all identical  B0365.3  863MPWDLYQLRAQWDSRAYNNVLDS
Xtropicalis  all identical  ENSXETG00000008125  883LPSRLLGIRLDWDDRSNNDVEDS
protein features
start (aa)end (aa)featuredetails 
864915TOPO_DOMExtracellular (Potential).lost
916935TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
936948TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
940940MOD_RESPhosphoserine; by PKA (By similarity).might get lost (downstream of altered splice site)
949967TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
968982TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
9831003TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
10041020TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 3030 / 3030
position (AA) of stopcodon in wt / mu AA sequence 1010 / 1010
position of stopcodon in wt / mu cDNA 3115 / 3115
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 86 / 86
chromosome 1
strand 1
last intron/exon boundary 3087
theoretical NMD boundary in CDS 2951
length of CDS 3030
coding sequence (CDS) position 2659
cDNA position
(for ins/del: last normal base / first normal base)
2744
gDNA position
(for ins/del: last normal base / first normal base)
20907
chromosomal position
(for ins/del: last normal base / first normal base)
160106455
original gDNA sequence snippet TACTGGGAATCCGCCTCGACTGGGATGACCGGACCATGAAT
altered gDNA sequence snippet TACTGGGAATCCGCCTCGACCGGGATGACCGGACCATGAAT
original cDNA sequence snippet TACTGGGAATCCGCCTCGACTGGGATGACCGGACCATGAAT
altered cDNA sequence snippet TACTGGGAATCCGCCTCGACCGGGATGACCGGACCATGAAT
wildtype AA sequence MGRGAGREYS PAATTAENGG GKKKQKEKEL DELKKEVAMD DHKLSLDELG RKYQVDLSKG
LTNQRAQDVL ARDGPNALTP PPTTPEWVKF CRQLFGGFSI LLWIGAILCF LAYGIQAAME
DEPSNDNLYL GVVLAAVVIV TGCFSYYQEA KSSKIMDSFK NMVPQQALVI REGEKMQINA
EEVVVGDLVE VKGGDRVPAD LRIISSHGCK VDNSSLTGES EPQTRSPEFT HENPLETRNI
CFFSTNCVEG TARGIVIATG DRTVMGRIAT LASGLEVGRT PIAMEIEHFI QLITGVAVFL
GVSFFVLSLI LGYSWLEAVI FLIGIIVANV PEGLLATVTV CLTLTAKRMA RKNCLVKNLE
AVETLGSTST ICSDKTGTLT QNRMTVAHMW FDNQIHEADT TEDQSGATFD KRSPTWTALS
RIAGLCNRAV FKAGQENISV SKRDTAGDAS ESALLKCIEL SCGSVRKMRD RNPKVAEIPF
NSTNKYQLSI HEREDSPQSH VLVMKGAPER ILDRCSTILV QGKEIPLDKE MQDAFQNAYM
ELGGLGERVL GFCQLNLPSG KFPRGFKFDT DELNFPTEKL CFVGLMSMID PPRAAVPDAV
GKCRSAGIKV IMVTGDHPIT AKAIAKGVGI ISEGNETVED IAARLNIPMS QVNPREAKAC
VVHGSDLKDM TSEQLDEILK NHTEIVFART SPQQKLIIVE GCQRQGAIVA VTGDGVNDSP
ALKKADIGIA MGISGSDVSK QAADMILLDD NFASIVTGVE EGRLIFDNLK KSIAYTLTSN
IPEITPFLLF IIANIPLPLG TVTILCIDLG TDMVPAISLA YEAAESDIMK RQPRNSQTDK
LVNERLISMA YGQIGMIQAL GGFFTYFVIL AENGFLPSRL LGIRLDWDDR TMNDLEDSYG
QEWTYEQRKV VEFTCHTAFF ASIVVVQWAD LIICKTRRNS VFQQGMKNKI LIFGLLEETA
LAAFLSYCPG MGVALRMYPL NLLIFIYDEV RKLILRRYPG GWVEKETYY*
mutated AA sequence MGRGAGREYS PAATTAENGG GKKKQKEKEL DELKKEVAMD DHKLSLDELG RKYQVDLSKG
LTNQRAQDVL ARDGPNALTP PPTTPEWVKF CRQLFGGFSI LLWIGAILCF LAYGIQAAME
DEPSNDNLYL GVVLAAVVIV TGCFSYYQEA KSSKIMDSFK NMVPQQALVI REGEKMQINA
EEVVVGDLVE VKGGDRVPAD LRIISSHGCK VDNSSLTGES EPQTRSPEFT HENPLETRNI
CFFSTNCVEG TARGIVIATG DRTVMGRIAT LASGLEVGRT PIAMEIEHFI QLITGVAVFL
GVSFFVLSLI LGYSWLEAVI FLIGIIVANV PEGLLATVTV CLTLTAKRMA RKNCLVKNLE
AVETLGSTST ICSDKTGTLT QNRMTVAHMW FDNQIHEADT TEDQSGATFD KRSPTWTALS
RIAGLCNRAV FKAGQENISV SKRDTAGDAS ESALLKCIEL SCGSVRKMRD RNPKVAEIPF
NSTNKYQLSI HEREDSPQSH VLVMKGAPER ILDRCSTILV QGKEIPLDKE MQDAFQNAYM
ELGGLGERVL GFCQLNLPSG KFPRGFKFDT DELNFPTEKL CFVGLMSMID PPRAAVPDAV
GKCRSAGIKV IMVTGDHPIT AKAIAKGVGI ISEGNETVED IAARLNIPMS QVNPREAKAC
VVHGSDLKDM TSEQLDEILK NHTEIVFART SPQQKLIIVE GCQRQGAIVA VTGDGVNDSP
ALKKADIGIA MGISGSDVSK QAADMILLDD NFASIVTGVE EGRLIFDNLK KSIAYTLTSN
IPEITPFLLF IIANIPLPLG TVTILCIDLG TDMVPAISLA YEAAESDIMK RQPRNSQTDK
LVNERLISMA YGQIGMIQAL GGFFTYFVIL AENGFLPSRL LGIRLDRDDR TMNDLEDSYG
QEWTYEQRKV VEFTCHTAFF ASIVVVQWAD LIICKTRRNS VFQQGMKNKI LIFGLLEETA
LAAFLSYCPG MGVALRMYPL NLLIFIYDEV RKLILRRYPG GWVEKETYY*
speed 1.19 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