MutationTaster - study a chromosomal position

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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 3.810748 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ATP1A2	disease_causing_automatic	0.999999946429366	simple_aae		affected	0	W887R	single base exchange	rs28933399		show file
ATP1A2	disease_causing_automatic	0.999999946429366	simple_aae		affected	0	W887R	single base exchange	rs28933399		show file

Taster files

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

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

	PhyloP	PhastCons
(flanking)	0.727	0.998
	4.347	1
(flanking)	5.173	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor increased	20898	wt: 0.20 / mu: 0.38	wt: GAATCCGCCTCGACT mu: GAATCCGCCTCGACC	ATCC\|gcct
Donor marginally increased	20907	wt: 0.9654 / mu: 0.9885 (marginal change - not scored)	wt: TCGACTGGGATGACC mu: TCGACCGGGATGACC	GACT\|ggga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

887

mutated

not conserved

887

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000017833

887

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000007097

887

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000010472

884

Dmelanogaster

all identical

FBgn0002921

908

Celegans

all identical

B0365.3

863

Xtropicalis

all identical

ENSXETG00000008125

883

protein features

start (aa)	end (aa)	feature	details
864	915	TOPO_DOM	Extracellular (Potential).	lost
916	935	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
936	948	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
940	940	MOD_RES	Phosphoserine; by PKA (By similarity).	might get lost (downstream of altered splice site)
949	967	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
968	982	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
983	1003	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1004	1020	TOPO_DOM	Cytoplasmic (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

strand

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

0.93 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

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

known variant

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.727	0.998
	4.347	1
(flanking)	5.173	1

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor increased	20898	wt: 0.20 / mu: 0.38	wt: GAATCCGCCTCGACT mu: GAATCCGCCTCGACC	ATCC\|gcct
Donor marginally increased	20907	wt: 0.9654 / mu: 0.9885 (marginal change - not scored)	wt: TCGACTGGGATGACC mu: TCGACCGGGATGACC	GACT\|ggga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

887

mutated

not conserved

887

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000017833

887

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000007097

887

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000010472

884

Dmelanogaster

all identical

FBgn0002921

908

Celegans

all identical

B0365.3

863

Xtropicalis

all identical

ENSXETG00000008125

883

protein features

start (aa)	end (aa)	feature	details
864	915	TOPO_DOM	Extracellular (Potential).	lost
916	935	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
936	948	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
940	940	MOD_RES	Phosphoserine; by PKA (By similarity).	might get lost (downstream of altered splice site)
949	967	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
968	982	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
983	1003	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
1004	1020	TOPO_DOM	Cytoplasmic (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

strand

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

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

0.89 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems