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 2.657795 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ATP1A2	disease_causing	0.999999999739368	simple_aae		affected		P979L	single base exchange	rs121918615		show file
ATP1A2	disease_causing	0.999999999969484	simple_aae		affected		P979L	single base exchange	rs121918615		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999739368 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs12925 (probable pathogenic)
known disease mutation at this position (HGMD CM041251)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:160109525C>TN/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.2936C>T
cDNA.3025C>T
g.23977C>T

AA changes

P979L Score: 98 explain score(s)

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

979

frameshift

known variant

Reference ID: rs121918615
Allele 'T' was neither found in ExAC nor 1000G.
known as potential disease variant: rs12925 (probable pathogenic for Familial hemiplegic migraine|Familial hemiplegic migraine type 2) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM041251)

known disease mutation at this position, please check HGMD for details (HGMD ID CM041251)
known disease mutation at this position, please check HGMD for details (HGMD ID CM041251)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.099	1
	5.099	1
(flanking)	-1.697	0.174

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 increased	23983	wt: 0.50 / mu: 0.61	wt: CCTCCGCATGTACCCGCTCAAGTGAGTGTCTCTTTCGGGCG mu: CCTCCGCATGTACCTGCTCAAGTGAGTGTCTCTTTCGGGCG	tcaa\|GTGA
Acc marginally increased	23973	wt: 0.3588 / mu: 0.3745 (marginal change - not scored)	wt: TGGGTGTAGCCCTCCGCATGTACCCGCTCAAGTGAGTGTCT mu: TGGGTGTAGCCCTCCGCATGTACCTGCTCAAGTGAGTGTCT	atgt\|ACCC
Donor marginally increased	23978	wt: 0.9855 / mu: 0.9877 (marginal change - not scored)	wt: TACCCGCTCAAGTGA mu: TACCTGCTCAAGTGA	CCCG\|ctca
Donor marginally decreased	23982	wt: 0.9712 / mu: 0.9658 (marginal change - not scored)	wt: CGCTCAAGTGAGTGT mu: TGCTCAAGTGAGTGT	CTCA\|agtg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

979

mutated

not conserved

979

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000017833

979

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000007097

979

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000010472

976

Dmelanogaster

all identical

FBgn0002921

1000

Celegans

not conserved

B0365.3

955

Xtropicalis

all identical

ENSXETG00000008125

975

protein features

start (aa)	end (aa)	feature	details
968	982	TOPO_DOM	Extracellular (Potential).	lost
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

2936

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

3025

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

23977

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

160109525

original gDNA sequence snippet

TGTAGCCCTCCGCATGTACCCGCTCAAGTGAGTGTCTCTTT

altered gDNA sequence snippet

TGTAGCCCTCCGCATGTACCTGCTCAAGTGAGTGTCTCTTT

original cDNA sequence snippet

TGTAGCCCTCCGCATGTACCCGCTCAAAGTCACCTGGTGGT

altered cDNA sequence snippet

TGTAGCCCTCCGCATGTACCTGCTCAAAGTCACCTGGTGGT

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

speed

0.31 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: 0.999999999969484 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs12925 (probable pathogenic)
known disease mutation at this position (HGMD CM041251)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:160109525C>TN/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.2936C>T
cDNA.3021C>T
g.23977C>T

AA changes

P979L Score: 98 explain score(s)

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

979

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)	5.099	1
	5.099	1
(flanking)	-1.697	0.174

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 increased	23983	wt: 0.50 / mu: 0.61	wt: CCTCCGCATGTACCCGCTCAAGTGAGTGTCTCTTTCGGGCG mu: CCTCCGCATGTACCTGCTCAAGTGAGTGTCTCTTTCGGGCG	tcaa\|GTGA
Acc marginally increased	23973	wt: 0.3588 / mu: 0.3745 (marginal change - not scored)	wt: TGGGTGTAGCCCTCCGCATGTACCCGCTCAAGTGAGTGTCT mu: TGGGTGTAGCCCTCCGCATGTACCTGCTCAAGTGAGTGTCT	atgt\|ACCC
Donor marginally increased	23978	wt: 0.9855 / mu: 0.9877 (marginal change - not scored)	wt: TACCCGCTCAAGTGA mu: TACCTGCTCAAGTGA	CCCG\|ctca
Donor marginally decreased	23982	wt: 0.9712 / mu: 0.9658 (marginal change - not scored)	wt: CGCTCAAGTGAGTGT mu: TGCTCAAGTGAGTGT	CTCA\|agtg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

979

mutated

not conserved

979

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000017833

979

LKVTWWFCAFPY

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000007097

979

LKVTWWFCAFPY

Ggallus

no homologue

Trubripes

no homologue

Drerio

all identical

ENSDARG00000010472

976

LKIMWWFCAFPY

Dmelanogaster

all identical

FBgn0002921

1000

Celegans

all identical

B0365.3

958

FSWWFCAL

Xtropicalis

all identical

ENSXETG00000008125

975

LKVTWWFCAFPY

protein features

start (aa)	end (aa)	feature	details
968	982	TOPO_DOM	Extracellular (Potential).	lost
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

2936

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

3021

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

23977

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

160109525

original gDNA sequence snippet

TGTAGCCCTCCGCATGTACCCGCTCAAGTGAGTGTCTCTTT

altered gDNA sequence snippet

TGTAGCCCTCCGCATGTACCTGCTCAAGTGAGTGTCTCTTT

original cDNA sequence snippet

TGTAGCCCTCCGCATGTACCCGCTCAACCTCCTCATCTTCA

altered cDNA sequence snippet

TGTAGCCCTCCGCATGTACCTGCTCAACCTCCTCATCTTCA

wildtype AA sequence

mutated AA sequence

speed

0.31 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems