Yum, tasty mutations...

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 2 transcript(s)...
Querying Taster for transcript #1: ENST00000361216
Querying Taster for transcript #2: ENST00000392233
MT speed 0 s - this script 2.690061 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
ATP1A2disease_causing_automatic0.999999999402525simple_aaeaffected0G301Rsingle base exchangers121918612show file
ATP1A2disease_causing_automatic0.999999999402525simple_aaeaffected0G301Rsingle base exchangers121918612show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999402525 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM045040)
  • known disease mutation: rs12922 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:160097494G>AN/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.901G>A
cDNA.990G>A
g.11946G>A
AA changes G301R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 301
frameshift no
known variant Reference ID: rs121918612
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs12922 (pathogenic for Familial hemiplegic migraine type 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM045040)

known disease mutation at this position, please check HGMD for details (HGMD ID CM045040)
known disease mutation at this position, please check HGMD for details (HGMD ID CM045040)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.2411
5.5941
(flanking)5.5941
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased11946wt: 0.33 / mu: 0.36wt: CAGGGGTCGCTGTATTCCTGGGGGTCTCCTTCTTCGTGCTC
mu: CAGGGGTCGCTGTATTCCTGAGGGTCTCCTTCTTCGTGCTC		 ctgg|GGGT
distance from splice site 117
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      301IQLITGVAVFLGVSFFVLSLILGY
mutated  not conserved    301RVSFFVLSLILG
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000017833  301GVSFFVLSLILG
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000007097  301GVSFFVLSLILG
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000010472  298GMSFFILSIILG
Dmelanogaster  all identical  FBgn0002921  321IHLITGVAVFLGVTFFVIAFILG
Celegans  all identical  B0365.3  281IHLITGVAVFLGISFFIIAFILG
Xtropicalis  all identical  ENSXETG00000008125  297IHIITGVAVFLGVSFF
protein features
start (aa)end (aa)featuredetails 
287306TRANSMEMHelical; (Potential).lost
307318TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
319336TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
337769TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
374374ACT_SITE4-aspartylphosphate intermediate (By similarity).might get lost (downstream of altered splice site)
570570MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
587587MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
650650MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
714714METALMagnesium (By similarity).might get lost (downstream of altered splice site)
718718METALMagnesium (By similarity).might get lost (downstream of altered splice site)
770789TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
790799TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
800820TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
821840TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
841863TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
864915TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
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 901
cDNA position
(for ins/del: last normal base / first normal base)		 990
gDNA position
(for ins/del: last normal base / first normal base)		 11946
chromosomal position
(for ins/del: last normal base / first normal base)		 160097494
original gDNA sequence snippet CAGGGGTCGCTGTATTCCTGGGGGTCTCCTTCTTCGTGCTC
altered gDNA sequence snippet CAGGGGTCGCTGTATTCCTGAGGGTCTCCTTCTTCGTGCTC
original cDNA sequence snippet CAGGGGTCGCTGTATTCCTGGGGGTCTCCTTCTTCGTGCTC
altered cDNA sequence snippet CAGGGGTCGCTGTATTCCTGAGGGTCTCCTTCTTCGTGCTC
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
RVSFFVLSLI 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
*
speed 0.54 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: 0.999999999402525 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM045040)
  • known disease mutation: rs12922 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:160097494G>AN/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.901G>A
cDNA.986G>A
g.11946G>A
AA changes G301R Score: 125 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 301
frameshift no
known variant Reference ID: rs121918612
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs12922 (pathogenic for Familial hemiplegic migraine type 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM045040)

known disease mutation at this position, please check HGMD for details (HGMD ID CM045040)
known disease mutation at this position, please check HGMD for details (HGMD ID CM045040)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.2411
5.5941
(flanking)5.5941
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased11946wt: 0.33 / mu: 0.36wt: CAGGGGTCGCTGTATTCCTGGGGGTCTCCTTCTTCGTGCTC
mu: CAGGGGTCGCTGTATTCCTGAGGGTCTCCTTCTTCGTGCTC		 ctgg|GGGT
distance from splice site 117
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      301IQLITGVAVFLGVSFFVLSLILGY
mutated  not conserved    301RVSFFVLSLILG
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000017833  301GVSFFVLSLILG
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000007097  301GVSFFVLSLILG
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000010472  298GMSFFILSIILG
Dmelanogaster  all identical  FBgn0002921  321IHLITGVAVFLGVTFFVIAFILG
Celegans  all identical  B0365.3  281IHLITGVAVFLGISFFIIAFILG
Xtropicalis  all identical  ENSXETG00000008125  297IHIITGVAVFLGVSFF
protein features
start (aa)end (aa)featuredetails 
287306TRANSMEMHelical; (Potential).lost
307318TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
319336TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
337769TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
374374ACT_SITE4-aspartylphosphate intermediate (By similarity).might get lost (downstream of altered splice site)
570570MOD_RESPhosphothreonine.might get lost (downstream of altered splice site)
587587MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
650650MOD_RESPhosphoserine (By similarity).might get lost (downstream of altered splice site)
714714METALMagnesium (By similarity).might get lost (downstream of altered splice site)
718718METALMagnesium (By similarity).might get lost (downstream of altered splice site)
770789TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
790799TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
800820TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
821840TOPO_DOMCytoplasmic (Potential).might get lost (downstream of altered splice site)
841863TRANSMEMHelical; (Potential).might get lost (downstream of altered splice site)
864915TOPO_DOMExtracellular (Potential).might get lost (downstream of altered splice site)
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 901
cDNA position
(for ins/del: last normal base / first normal base)		 986
gDNA position
(for ins/del: last normal base / first normal base)		 11946
chromosomal position
(for ins/del: last normal base / first normal base)		 160097494
original gDNA sequence snippet CAGGGGTCGCTGTATTCCTGGGGGTCTCCTTCTTCGTGCTC
altered gDNA sequence snippet CAGGGGTCGCTGTATTCCTGAGGGTCTCCTTCTTCGTGCTC
original cDNA sequence snippet CAGGGGTCGCTGTATTCCTGGGGGTCTCCTTCTTCGTGCTC
altered cDNA sequence snippet CAGGGGTCGCTGTATTCCTGAGGGTCTCCTTCTTCGTGCTC
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
RVSFFVLSLI 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*
speed 0.59 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

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