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 3.565385 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ATP1A2	disease_causing	0.999999434485274	simple_aae		affected		R689Q	single base exchange	rs28933401		show file
ATP1A2	disease_causing	0.999999434485274	simple_aae		affected		R689Q	single base exchange	rs28933401		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999434485274 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs12920 (probable pathogenic)
known disease mutation at this position (HGMD CM032182)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:160105036G>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.2066G>A
cDNA.2155G>A
g.19488G>A

AA changes

R689Q Score: 43 explain score(s)

position(s) of altered AA
if AA alteration in CDS

689

frameshift

known variant

Reference ID: rs28933401
Allele 'A' was neither found in ExAC nor 1000G.
known as potential disease variant: rs12920 (probable pathogenic for Familial hemiplegic migraine type 2|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM032182)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032182)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032182)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.482	0.995
	5.471	1
(flanking)	0.117	0.997

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
Acc marginally increased	19491	wt: 0.9216 / mu: 0.9501 (marginal change - not scored)	wt: AGAGATCGTCTTTGCTCGAACGTCTCCCCAGCAGAAGCTCA mu: AGAGATCGTCTTTGCTCAAACGTCTCCCCAGCAGAAGCTCA	gaac\|GTCT
Acc increased	19488	wt: 0.42 / mu: 0.46	wt: CACAGAGATCGTCTTTGCTCGAACGTCTCCCCAGCAGAAGC mu: CACAGAGATCGTCTTTGCTCAAACGTCTCCCCAGCAGAAGC	ctcg\|AACG
Acc marginally increased	19489	wt: 0.4909 / mu: 0.5009 (marginal change - not scored)	wt: ACAGAGATCGTCTTTGCTCGAACGTCTCCCCAGCAGAAGCT mu: ACAGAGATCGTCTTTGCTCAAACGTCTCCCCAGCAGAAGCT	tcga\|ACGT
Donor marginally increased	19486	wt: 0.8723 / mu: 0.9549 (marginal change - not scored)	wt: TTTGCTCGAACGTCT mu: TTTGCTCAAACGTCT	TGCT\|cgaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

689

mutated

all conserved

689

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000017833

689

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000007097

689

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000010472

686

Dmelanogaster

all identical

FBgn0002921

710

Celegans

all identical

B0365.3

665

Xtropicalis

all identical

ENSXETG00000008125

685

protein features

start (aa)	end (aa)	feature	details
337	769	TOPO_DOM	Cytoplasmic (Potential).	lost
714	714	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
718	718	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
770	789	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
790	799	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
800	820	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
821	840	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
841	863	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
864	915	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
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

2066

cDNA position
(for ins/del: last normal base / first normal base)

2155

gDNA position
(for ins/del: last normal base / first normal base)

19488

chromosomal position
(for ins/del: last normal base / first normal base)

160105036

original gDNA sequence snippet

CACAGAGATCGTCTTTGCTCGAACGTCTCCCCAGCAGAAGC

altered gDNA sequence snippet

CACAGAGATCGTCTTTGCTCAAACGTCTCCCCAGCAGAAGC

original cDNA sequence snippet

CACAGAGATCGTCTTTGCTCGAACGTCTCCCCAGCAGAAGC

altered cDNA sequence snippet

CACAGAGATCGTCTTTGCTCAAACGTCTCCCCAGCAGAAGC

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 NHTEIVFAQT 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

0.85 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: 0.999999434485274 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs12920 (probable pathogenic)
known disease mutation at this position (HGMD CM032182)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:160105036G>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.2066G>A
cDNA.2151G>A
g.19488G>A

AA changes

R689Q Score: 43 explain score(s)

position(s) of altered AA
if AA alteration in CDS

689

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)	1.482	0.995
	5.471	1
(flanking)	0.117	0.997

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
Acc marginally increased	19491	wt: 0.9216 / mu: 0.9501 (marginal change - not scored)	wt: AGAGATCGTCTTTGCTCGAACGTCTCCCCAGCAGAAGCTCA mu: AGAGATCGTCTTTGCTCAAACGTCTCCCCAGCAGAAGCTCA	gaac\|GTCT
Acc increased	19488	wt: 0.42 / mu: 0.46	wt: CACAGAGATCGTCTTTGCTCGAACGTCTCCCCAGCAGAAGC mu: CACAGAGATCGTCTTTGCTCAAACGTCTCCCCAGCAGAAGC	ctcg\|AACG
Acc marginally increased	19489	wt: 0.4909 / mu: 0.5009 (marginal change - not scored)	wt: ACAGAGATCGTCTTTGCTCGAACGTCTCCCCAGCAGAAGCT mu: ACAGAGATCGTCTTTGCTCAAACGTCTCCCCAGCAGAAGCT	tcga\|ACGT
Donor marginally increased	19486	wt: 0.8723 / mu: 0.9549 (marginal change - not scored)	wt: TTTGCTCGAACGTCT mu: TTTGCTCAAACGTCT	TGCT\|cgaa

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

689

mutated

all conserved

689

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000017833

689

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000007097

689

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000010472

686

Dmelanogaster

all identical

FBgn0002921

710

Celegans

all identical

B0365.3

665

Xtropicalis

all identical

ENSXETG00000008125

685

protein features

start (aa)	end (aa)	feature	details
337	769	TOPO_DOM	Cytoplasmic (Potential).	lost
714	714	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
718	718	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
770	789	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
790	799	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
800	820	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
821	840	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
841	863	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
864	915	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
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

2066

cDNA position
(for ins/del: last normal base / first normal base)

2151

gDNA position
(for ins/del: last normal base / first normal base)

19488

chromosomal position
(for ins/del: last normal base / first normal base)

160105036

original gDNA sequence snippet

CACAGAGATCGTCTTTGCTCGAACGTCTCCCCAGCAGAAGC

altered gDNA sequence snippet

CACAGAGATCGTCTTTGCTCAAACGTCTCCCCAGCAGAAGC

original cDNA sequence snippet

CACAGAGATCGTCTTTGCTCGAACGTCTCCCCAGCAGAAGC

altered cDNA sequence snippet

CACAGAGATCGTCTTTGCTCAAACGTCTCCCCAGCAGAAGC

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 NHTEIVFAQT 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

0.66 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems