MutationTaster - study a chromosomal position

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 3 transcript(s)...
Querying Taster for transcript #1: ENST00000302102
Querying Taster for transcript #2: ENST00000545399
Querying Taster for transcript #3: ENST00000543770
MT speed 0 s - this script 3.303929 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
ATP1A3	disease_causing_automatic	0.999999998821359	simple_aae		affected	0	E277K	single base exchange	rs80356533		show file
ATP1A3	disease_causing_automatic	0.999999999330588	simple_aae		affected	0	E290K	single base exchange	rs80356533		show file
ATP1A3	disease_causing_automatic	0.999999999330588	simple_aae		affected	0	E288K	single base exchange	rs80356533		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999998821359 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM042304)
known disease mutation: rs12911 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:42489234C>TN/A show variant in all transcripts IGV

HGNC symbol

ATP1A3

Ensembl transcript ID

ENST00000302102

Genbank transcript ID

NM_152296

UniProt peptide

P13637

alteration type

single base exchange

alteration region

CDS

DNA changes

c.829G>A
cDNA.980G>A
g.9151G>A

AA changes

E277K Score: 56 explain score(s)

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

277

frameshift

known variant

Reference ID: rs80356533
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs12911 (pathogenic for Dystonia 12) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM042304)

known disease mutation at this position, please check HGMD for details (HGMD ID CM042304)
known disease mutation at this position, please check HGMD for details (HGMD ID CM042304)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.155	1
	5.03	1
(flanking)	-1.153	0.74

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	9153	wt: 0.35 / mu: 0.73	wt: ATCGAGATTGAGCAC mu: ATCAAGATTGAGCAC	CGAG\|attg
Donor gained	9147	0.94	mu: ATCGCCATCAAGATT	CGCC\|atca

distance from splice site

105

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

277

mutated

all conserved

277

Ptroglodytes

no alignment

ENSPTRG00000011041

n/a

Mmulatta

all identical

ENSMMUG00000017427

277

Fcatus

all identical

ENSFCAG00000012729

177

Mmusculus

all identical

ENSMUSG00000040907

277

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000008243

284

Drerio

all identical

ENSDARG00000018259

287

Dmelanogaster

all identical

FBgn0002921

305

Celegans

all identical

B0365.3

265

Xtropicalis

all identical

ENSXETG00000023811

289

protein features

start (aa)	end (aa)	feature	details
143	278	TOPO_DOM	Cytoplasmic (Potential).	lost
279	298	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
299	310	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
311	328	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
329	762	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
336	336	CONFLICT	L -> V (in Ref. 1; AAA51798, 2; CAA31390, 5; AAA52285 and 7; AAA58380).	might get lost (downstream of altered splice site)
366	366	ACT_SITE	4-aspartylphosphate intermediate (By similarity).	might get lost (downstream of altered splice site)
368	368	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
380	380	CONFLICT	H -> T (in Ref. 5; AAA52285).	might get lost (downstream of altered splice site)
421	421	CONFLICT	A -> P (in Ref. 7; AAA58380).	might get lost (downstream of altered splice site)
430	430	CONFLICT	I -> M (in Ref. 2; CAA31390).	might get lost (downstream of altered splice site)
493	493	MOD_RES	Phosphotyrosine (By similarity).	might get lost (downstream of altered splice site)
548	548	MOD_RES	Phosphotyrosine (By similarity).	might get lost (downstream of altered splice site)
549	549	MOD_RES	Phosphotyrosine (By similarity).	might get lost (downstream of altered splice site)
555	557	CONFLICT	FPK -> YPQ (in Ref. 1; AAA51798, 2; CAA31390 and 5; AAA52286).	might get lost (downstream of altered splice site)
577	577	CONFLICT	G -> P (in Ref. 1; AAA51798).	might get lost (downstream of altered splice site)
583	583	CONFLICT	D -> G (in Ref. 1; AAA51798, 2; CAA31390 and 5; AAA52286).	might get lost (downstream of altered splice site)
707	707	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
711	711	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
763	782	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
783	792	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
793	813	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
814	833	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
834	856	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
857	908	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
909	928	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
919	919	CONFLICT	V -> A (in Ref. 5; AAA52286).	might get lost (downstream of altered splice site)
929	941	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
933	933	MOD_RES	Phosphoserine; by PKA (By similarity).	might get lost (downstream of altered splice site)
942	960	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
944	944	CONFLICT	L -> M (in Ref. 5; AAA52286).	might get lost (downstream of altered splice site)
961	975	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
976	996	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
982	982	CONFLICT	F -> S (in Ref. 2; CAA31390).	might get lost (downstream of altered splice site)
997	1013	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1006	1006	CONFLICT	W -> S (in Ref. 1; AAA51798).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3042 / 3042

position (AA) of stopcodon in wt / mu AA sequence

1014 / 1014

position of stopcodon in wt / mu cDNA

3193 / 3193

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

152 / 152

chromosome

strand

-1

last intron/exon boundary

3165

theoretical NMD boundary in CDS

2963

length of CDS

3042

coding sequence (CDS) position

829

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

980

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

9151

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

42489234

original gDNA sequence snippet

GCAAGACGCCCATCGCCATCGAGATTGAGCACTTCATCCAG

altered gDNA sequence snippet

GCAAGACGCCCATCGCCATCAAGATTGAGCACTTCATCCAG

original cDNA sequence snippet

GCAAGACGCCCATCGCCATCGAGATTGAGCACTTCATCCAG

altered cDNA sequence snippet

GCAAGACGCCCATCGCCATCAAGATTGAGCACTTCATCCAG

wildtype AA sequence

MGDKKDDKDS PKKNKGKERR DLDDLKKEVA MTEHKMSVEE VCRKYNTDCV QGLTHSKAQE
ILARDGPNAL TPPPTTPEWV KFCRQLFGGF SILLWIGAIL CFLAYGIQAG TEDDPSGDNL
YLGIVLAAVV IITGCFSYYQ EAKSSKIMES FKNMVPQQAL VIREGEKMQV NAEEVVVGDL
VEIKGGDRVP ADLRIISAHG CKVDNSSLTG ESEPQTRSPD CTHDNPLETR NITFFSTNCV
EGTARGVVVA TGDRTVMGRI ATLASGLEVG KTPIAIEIEH FIQLITGVAV FLGVSFFILS
LILGYTWLEA VIFLIGIIVA NVPEGLLATV TVCLTLTAKR MARKNCLVKN LEAVETLGST
STICSDKTGT LTQNRMTVAH MWFDNQIHEA DTTEDQSGTS FDKSSHTWVA LSHIAGLCNR
AVFKGGQDNI PVLKRDVAGD ASESALLKCI ELSSGSVKLM RERNKKVAEI PFNSTNKYQL
SIHETEDPND NRYLLVMKGA PERILDRCST ILLQGKEQPL DEEMKEAFQN AYLELGGLGE
RVLGFCHYYL PEEQFPKGFA FDCDDVNFTT DNLCFVGLMS MIDPPRAAVP DAVGKCRSAG
IKVIMVTGDH PITAKAIAKG VGIISEGNET VEDIAARLNI PVSQVNPRDA KACVIHGTDL
KDFTSEQIDE ILQNHTEIVF ARTSPQQKLI IVEGCQRQGA IVAVTGDGVN DSPALKKADI
GVAMGIAGSD VSKQAADMIL LDDNFASIVT GVEEGRLIFD NLKKSIAYTL TSNIPEITPF
LLFIMANIPL PLGTITILCI DLGTDMVPAI SLAYEAAESD IMKRQPRNPR TDKLVNERLI
SMAYGQIGMI QALGGFFSYF VILAENGFLP GNLVGIRLNW DDRTVNDLED SYGQQWTYEQ
RKVVEFTCHT AFFVSIVVVQ WADLIICKTR RNSVFQQGMK NKILIFGLFE ETALAAFLSY
CPGMDVALRM YPLKPSWWFC AFPYSFLIFV YDEIRKLILR RNPGGWVEKE TYY*

mutated AA sequence

MGDKKDDKDS PKKNKGKERR DLDDLKKEVA MTEHKMSVEE VCRKYNTDCV QGLTHSKAQE
ILARDGPNAL TPPPTTPEWV KFCRQLFGGF SILLWIGAIL CFLAYGIQAG TEDDPSGDNL
YLGIVLAAVV IITGCFSYYQ EAKSSKIMES FKNMVPQQAL VIREGEKMQV NAEEVVVGDL
VEIKGGDRVP ADLRIISAHG CKVDNSSLTG ESEPQTRSPD CTHDNPLETR NITFFSTNCV
EGTARGVVVA TGDRTVMGRI ATLASGLEVG KTPIAIKIEH FIQLITGVAV FLGVSFFILS
LILGYTWLEA VIFLIGIIVA NVPEGLLATV TVCLTLTAKR MARKNCLVKN LEAVETLGST
STICSDKTGT LTQNRMTVAH MWFDNQIHEA DTTEDQSGTS FDKSSHTWVA LSHIAGLCNR
AVFKGGQDNI PVLKRDVAGD ASESALLKCI ELSSGSVKLM RERNKKVAEI PFNSTNKYQL
SIHETEDPND NRYLLVMKGA PERILDRCST ILLQGKEQPL DEEMKEAFQN AYLELGGLGE
RVLGFCHYYL PEEQFPKGFA FDCDDVNFTT DNLCFVGLMS MIDPPRAAVP DAVGKCRSAG
IKVIMVTGDH PITAKAIAKG VGIISEGNET VEDIAARLNI PVSQVNPRDA KACVIHGTDL
KDFTSEQIDE ILQNHTEIVF ARTSPQQKLI IVEGCQRQGA IVAVTGDGVN DSPALKKADI
GVAMGIAGSD VSKQAADMIL LDDNFASIVT GVEEGRLIFD NLKKSIAYTL TSNIPEITPF
LLFIMANIPL PLGTITILCI DLGTDMVPAI SLAYEAAESD IMKRQPRNPR TDKLVNERLI
SMAYGQIGMI QALGGFFSYF VILAENGFLP GNLVGIRLNW DDRTVNDLED SYGQQWTYEQ
RKVVEFTCHT AFFVSIVVVQ WADLIICKTR RNSVFQQGMK NKILIFGLFE ETALAAFLSY
CPGMDVALRM YPLKPSWWFC AFPYSFLIFV YDEIRKLILR RNPGGWVEKE TYY*

speed

0.50 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: 0.999999999330588 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM042304)
known disease mutation: rs12911 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:42489234C>TN/A show variant in all transcripts IGV

HGNC symbol

ATP1A3

Ensembl transcript ID

ENST00000545399

Genbank transcript ID

NM_001256214

UniProt peptide

P13637

alteration type

single base exchange

alteration region

CDS

DNA changes

c.868G>A
cDNA.1022G>A
g.9151G>A

AA changes

E290K Score: 56 explain score(s)

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

290

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)	4.155	1
	5.03	1
(flanking)	-1.153	0.74

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	9153	wt: 0.35 / mu: 0.73	wt: ATCGAGATTGAGCAC mu: ATCAAGATTGAGCAC	CGAG\|attg
Donor gained	9147	0.94	mu: ATCGCCATCAAGATT	CGCC\|atca

distance from splice site

105

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

290

mutated

all conserved

290

Ptroglodytes

no alignment

ENSPTRG00000011041

n/a

Mmulatta

all identical

ENSMMUG00000017427

277

Fcatus

all identical

ENSFCAG00000012729

177

Mmusculus

all identical

ENSMUSG00000040907

277

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000008243

284

Drerio

all identical

ENSDARG00000018259

287

Dmelanogaster

all identical

FBgn0002921

305

Celegans

all identical

B0365.3

265

Xtropicalis

all identical

ENSXETG00000023811

289

protein features

start (aa)	end (aa)	feature	details
279	298	TRANSMEM	Helical; (Potential).	lost
299	310	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
311	328	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
329	762	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
336	336	CONFLICT	L -> V (in Ref. 1; AAA51798, 2; CAA31390, 5; AAA52285 and 7; AAA58380).	might get lost (downstream of altered splice site)
366	366	ACT_SITE	4-aspartylphosphate intermediate (By similarity).	might get lost (downstream of altered splice site)
368	368	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
380	380	CONFLICT	H -> T (in Ref. 5; AAA52285).	might get lost (downstream of altered splice site)
421	421	CONFLICT	A -> P (in Ref. 7; AAA58380).	might get lost (downstream of altered splice site)
430	430	CONFLICT	I -> M (in Ref. 2; CAA31390).	might get lost (downstream of altered splice site)
493	493	MOD_RES	Phosphotyrosine (By similarity).	might get lost (downstream of altered splice site)
548	548	MOD_RES	Phosphotyrosine (By similarity).	might get lost (downstream of altered splice site)
549	549	MOD_RES	Phosphotyrosine (By similarity).	might get lost (downstream of altered splice site)
555	557	CONFLICT	FPK -> YPQ (in Ref. 1; AAA51798, 2; CAA31390 and 5; AAA52286).	might get lost (downstream of altered splice site)
577	577	CONFLICT	G -> P (in Ref. 1; AAA51798).	might get lost (downstream of altered splice site)
583	583	CONFLICT	D -> G (in Ref. 1; AAA51798, 2; CAA31390 and 5; AAA52286).	might get lost (downstream of altered splice site)
707	707	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
711	711	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
763	782	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
783	792	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
793	813	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
814	833	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
834	856	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
857	908	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
909	928	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
919	919	CONFLICT	V -> A (in Ref. 5; AAA52286).	might get lost (downstream of altered splice site)
929	941	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
933	933	MOD_RES	Phosphoserine; by PKA (By similarity).	might get lost (downstream of altered splice site)
942	960	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
944	944	CONFLICT	L -> M (in Ref. 5; AAA52286).	might get lost (downstream of altered splice site)
961	975	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
976	996	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
982	982	CONFLICT	F -> S (in Ref. 2; CAA31390).	might get lost (downstream of altered splice site)
997	1013	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1006	1006	CONFLICT	W -> S (in Ref. 1; AAA51798).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3081 / 3081

position (AA) of stopcodon in wt / mu AA sequence

1027 / 1027

position of stopcodon in wt / mu cDNA

3235 / 3235

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

155 / 155

chromosome

strand

-1

last intron/exon boundary

3207

theoretical NMD boundary in CDS

3002

length of CDS

3081

coding sequence (CDS) position

868

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

1022

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

9151

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

42489234

original gDNA sequence snippet

GCAAGACGCCCATCGCCATCGAGATTGAGCACTTCATCCAG

altered gDNA sequence snippet

GCAAGACGCCCATCGCCATCAAGATTGAGCACTTCATCCAG

original cDNA sequence snippet

GCAAGACGCCCATCGCCATCGAGATTGAGCACTTCATCCAG

altered cDNA sequence snippet

GCAAGACGCCCATCGCCATCAAGATTGAGCACTTCATCCAG

wildtype AA sequence

MGSGGSDSYR IATSQDKKDD KDSPKKNKGK ERRDLDDLKK EVAMTEHKMS VEEVCRKYNT
DCVQGLTHSK AQEILARDGP NALTPPPTTP EWVKFCRQLF GGFSILLWIG AILCFLAYGI
QAGTEDDPSG DNLYLGIVLA AVVIITGCFS YYQEAKSSKI MESFKNMVPQ QALVIREGEK
MQVNAEEVVV GDLVEIKGGD RVPADLRIIS AHGCKVDNSS LTGESEPQTR SPDCTHDNPL
ETRNITFFST NCVEGTARGV VVATGDRTVM GRIATLASGL EVGKTPIAIE IEHFIQLITG
VAVFLGVSFF ILSLILGYTW LEAVIFLIGI IVANVPEGLL ATVTVCLTLT AKRMARKNCL
VKNLEAVETL GSTSTICSDK TGTLTQNRMT VAHMWFDNQI HEADTTEDQS GTSFDKSSHT
WVALSHIAGL CNRAVFKGGQ DNIPVLKRDV AGDASESALL KCIELSSGSV KLMRERNKKV
AEIPFNSTNK YQLSIHETED PNDNRYLLVM KGAPERILDR CSTILLQGKE QPLDEEMKEA
FQNAYLELGG LGERVLGFCH YYLPEEQFPK GFAFDCDDVN FTTDNLCFVG LMSMIDPPRA
AVPDAVGKCR SAGIKVIMVT GDHPITAKAI AKGVGIISEG NETVEDIAAR LNIPVSQVNP
RDAKACVIHG TDLKDFTSEQ IDEILQNHTE IVFARTSPQQ KLIIVEGCQR QGAIVAVTGD
GVNDSPALKK ADIGVAMGIA GSDVSKQAAD MILLDDNFAS IVTGVEEGRL IFDNLKKSIA
YTLTSNIPEI TPFLLFIMAN IPLPLGTITI LCIDLGTDMV PAISLAYEAA ESDIMKRQPR
NPRTDKLVNE RLISMAYGQI GMIQALGGFF SYFVILAENG FLPGNLVGIR LNWDDRTVND
LEDSYGQQWT YEQRKVVEFT CHTAFFVSIV VVQWADLIIC KTRRNSVFQQ GMKNKILIFG
LFEETALAAF LSYCPGMDVA LRMYPLKPSW WFCAFPYSFL IFVYDEIRKL ILRRNPGGWV
EKETYY*

mutated AA sequence

MGSGGSDSYR IATSQDKKDD KDSPKKNKGK ERRDLDDLKK EVAMTEHKMS VEEVCRKYNT
DCVQGLTHSK AQEILARDGP NALTPPPTTP EWVKFCRQLF GGFSILLWIG AILCFLAYGI
QAGTEDDPSG DNLYLGIVLA AVVIITGCFS YYQEAKSSKI MESFKNMVPQ QALVIREGEK
MQVNAEEVVV GDLVEIKGGD RVPADLRIIS AHGCKVDNSS LTGESEPQTR SPDCTHDNPL
ETRNITFFST NCVEGTARGV VVATGDRTVM GRIATLASGL EVGKTPIAIK IEHFIQLITG
VAVFLGVSFF ILSLILGYTW LEAVIFLIGI IVANVPEGLL ATVTVCLTLT AKRMARKNCL
VKNLEAVETL GSTSTICSDK TGTLTQNRMT VAHMWFDNQI HEADTTEDQS GTSFDKSSHT
WVALSHIAGL CNRAVFKGGQ DNIPVLKRDV AGDASESALL KCIELSSGSV KLMRERNKKV
AEIPFNSTNK YQLSIHETED PNDNRYLLVM KGAPERILDR CSTILLQGKE QPLDEEMKEA
FQNAYLELGG LGERVLGFCH YYLPEEQFPK GFAFDCDDVN FTTDNLCFVG LMSMIDPPRA
AVPDAVGKCR SAGIKVIMVT GDHPITAKAI AKGVGIISEG NETVEDIAAR LNIPVSQVNP
RDAKACVIHG TDLKDFTSEQ IDEILQNHTE IVFARTSPQQ KLIIVEGCQR QGAIVAVTGD
GVNDSPALKK ADIGVAMGIA GSDVSKQAAD MILLDDNFAS IVTGVEEGRL IFDNLKKSIA
YTLTSNIPEI TPFLLFIMAN IPLPLGTITI LCIDLGTDMV PAISLAYEAA ESDIMKRQPR
NPRTDKLVNE RLISMAYGQI GMIQALGGFF SYFVILAENG FLPGNLVGIR LNWDDRTVND
LEDSYGQQWT YEQRKVVEFT CHTAFFVSIV VVQWADLIIC KTRRNSVFQQ GMKNKILIFG
LFEETALAAF LSYCPGMDVA LRMYPLKPSW WFCAFPYSFL IFVYDEIRKL ILRRNPGGWV
EKETYY*

speed

0.53 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999330588 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM042304)
known disease mutation: rs12911 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr19:42489234C>TN/A show variant in all transcripts IGV

HGNC symbol

ATP1A3

Ensembl transcript ID

ENST00000543770

Genbank transcript ID

NM_001256213

UniProt peptide

P13637

alteration type

single base exchange

alteration region

CDS

DNA changes

c.862G>A
cDNA.898G>A
g.9151G>A

AA changes

E288K Score: 56 explain score(s)

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

288

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)	4.155	1
	5.03	1
(flanking)	-1.153	0.74

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	9153	wt: 0.35 / mu: 0.73	wt: ATCGAGATTGAGCAC mu: ATCAAGATTGAGCAC	CGAG\|attg
Donor gained	9147	0.94	mu: ATCGCCATCAAGATT	CGCC\|atca

distance from splice site

105

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

288

mutated

all conserved

288

Ptroglodytes

no alignment

ENSPTRG00000011041

n/a

Mmulatta

all identical

ENSMMUG00000017427

277

Fcatus

all identical

ENSFCAG00000012729

177

Mmusculus

all identical

ENSMUSG00000040907

277

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000008243

284

Drerio

all identical

ENSDARG00000018259

287

Dmelanogaster

all identical

FBgn0002921

305

Celegans

all identical

B0365.3

265

Xtropicalis

all identical

ENSXETG00000023811

289

protein features

start (aa)	end (aa)	feature	details
279	298	TRANSMEM	Helical; (Potential).	lost
299	310	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
311	328	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
329	762	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
336	336	CONFLICT	L -> V (in Ref. 1; AAA51798, 2; CAA31390, 5; AAA52285 and 7; AAA58380).	might get lost (downstream of altered splice site)
366	366	ACT_SITE	4-aspartylphosphate intermediate (By similarity).	might get lost (downstream of altered splice site)
368	368	MOD_RES	Phosphothreonine (By similarity).	might get lost (downstream of altered splice site)
380	380	CONFLICT	H -> T (in Ref. 5; AAA52285).	might get lost (downstream of altered splice site)
421	421	CONFLICT	A -> P (in Ref. 7; AAA58380).	might get lost (downstream of altered splice site)
430	430	CONFLICT	I -> M (in Ref. 2; CAA31390).	might get lost (downstream of altered splice site)
493	493	MOD_RES	Phosphotyrosine (By similarity).	might get lost (downstream of altered splice site)
548	548	MOD_RES	Phosphotyrosine (By similarity).	might get lost (downstream of altered splice site)
549	549	MOD_RES	Phosphotyrosine (By similarity).	might get lost (downstream of altered splice site)
555	557	CONFLICT	FPK -> YPQ (in Ref. 1; AAA51798, 2; CAA31390 and 5; AAA52286).	might get lost (downstream of altered splice site)
577	577	CONFLICT	G -> P (in Ref. 1; AAA51798).	might get lost (downstream of altered splice site)
583	583	CONFLICT	D -> G (in Ref. 1; AAA51798, 2; CAA31390 and 5; AAA52286).	might get lost (downstream of altered splice site)
707	707	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
711	711	METAL	Magnesium (By similarity).	might get lost (downstream of altered splice site)
763	782	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
783	792	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
793	813	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
814	833	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
834	856	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
857	908	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
909	928	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
919	919	CONFLICT	V -> A (in Ref. 5; AAA52286).	might get lost (downstream of altered splice site)
929	941	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
933	933	MOD_RES	Phosphoserine; by PKA (By similarity).	might get lost (downstream of altered splice site)
942	960	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
944	944	CONFLICT	L -> M (in Ref. 5; AAA52286).	might get lost (downstream of altered splice site)
961	975	TOPO_DOM	Extracellular (Potential).	might get lost (downstream of altered splice site)
976	996	TRANSMEM	Helical; (Potential).	might get lost (downstream of altered splice site)
982	982	CONFLICT	F -> S (in Ref. 2; CAA31390).	might get lost (downstream of altered splice site)
997	1013	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
1006	1006	CONFLICT	W -> S (in Ref. 1; AAA51798).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

3075 / 3075

position (AA) of stopcodon in wt / mu AA sequence

1025 / 1025

position of stopcodon in wt / mu cDNA

3111 / 3111

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

37 / 37

chromosome

strand

-1

last intron/exon boundary

3083

theoretical NMD boundary in CDS

2996

length of CDS

3075

coding sequence (CDS) position

862

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

898

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

9151

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

42489234

original gDNA sequence snippet

GCAAGACGCCCATCGCCATCGAGATTGAGCACTTCATCCAG

altered gDNA sequence snippet

GCAAGACGCCCATCGCCATCAAGATTGAGCACTTCATCCAG

original cDNA sequence snippet

GCAAGACGCCCATCGCCATCGAGATTGAGCACTTCATCCAG

altered cDNA sequence snippet

GCAAGACGCCCATCGCCATCAAGATTGAGCACTTCATCCAG

wildtype AA sequence

MGGWEEERNR RATDKKDDKD SPKKNKGKER RDLDDLKKEV AMTEHKMSVE EVCRKYNTDC
VQGLTHSKAQ EILARDGPNA LTPPPTTPEW VKFCRQLFGG FSILLWIGAI LCFLAYGIQA
GTEDDPSGDN LYLGIVLAAV VIITGCFSYY QEAKSSKIME SFKNMVPQQA LVIREGEKMQ
VNAEEVVVGD LVEIKGGDRV PADLRIISAH GCKVDNSSLT GESEPQTRSP DCTHDNPLET
RNITFFSTNC VEGTARGVVV ATGDRTVMGR IATLASGLEV GKTPIAIEIE HFIQLITGVA
VFLGVSFFIL SLILGYTWLE AVIFLIGIIV ANVPEGLLAT VTVCLTLTAK RMARKNCLVK
NLEAVETLGS TSTICSDKTG TLTQNRMTVA HMWFDNQIHE ADTTEDQSGT SFDKSSHTWV
ALSHIAGLCN RAVFKGGQDN IPVLKRDVAG DASESALLKC IELSSGSVKL MRERNKKVAE
IPFNSTNKYQ LSIHETEDPN DNRYLLVMKG APERILDRCS TILLQGKEQP LDEEMKEAFQ
NAYLELGGLG ERVLGFCHYY LPEEQFPKGF AFDCDDVNFT TDNLCFVGLM SMIDPPRAAV
PDAVGKCRSA GIKVIMVTGD HPITAKAIAK GVGIISEGNE TVEDIAARLN IPVSQVNPRD
AKACVIHGTD LKDFTSEQID EILQNHTEIV FARTSPQQKL IIVEGCQRQG AIVAVTGDGV
NDSPALKKAD IGVAMGIAGS DVSKQAADMI LLDDNFASIV TGVEEGRLIF DNLKKSIAYT
LTSNIPEITP FLLFIMANIP LPLGTITILC IDLGTDMVPA ISLAYEAAES DIMKRQPRNP
RTDKLVNERL ISMAYGQIGM IQALGGFFSY FVILAENGFL PGNLVGIRLN WDDRTVNDLE
DSYGQQWTYE QRKVVEFTCH TAFFVSIVVV QWADLIICKT RRNSVFQQGM KNKILIFGLF
EETALAAFLS YCPGMDVALR MYPLKPSWWF CAFPYSFLIF VYDEIRKLIL RRNPGGWVEK
ETYY*

mutated AA sequence

MGGWEEERNR RATDKKDDKD SPKKNKGKER RDLDDLKKEV AMTEHKMSVE EVCRKYNTDC
VQGLTHSKAQ EILARDGPNA LTPPPTTPEW VKFCRQLFGG FSILLWIGAI LCFLAYGIQA
GTEDDPSGDN LYLGIVLAAV VIITGCFSYY QEAKSSKIME SFKNMVPQQA LVIREGEKMQ
VNAEEVVVGD LVEIKGGDRV PADLRIISAH GCKVDNSSLT GESEPQTRSP DCTHDNPLET
RNITFFSTNC VEGTARGVVV ATGDRTVMGR IATLASGLEV GKTPIAIKIE HFIQLITGVA
VFLGVSFFIL SLILGYTWLE AVIFLIGIIV ANVPEGLLAT VTVCLTLTAK RMARKNCLVK
NLEAVETLGS TSTICSDKTG TLTQNRMTVA HMWFDNQIHE ADTTEDQSGT SFDKSSHTWV
ALSHIAGLCN RAVFKGGQDN IPVLKRDVAG DASESALLKC IELSSGSVKL MRERNKKVAE
IPFNSTNKYQ LSIHETEDPN DNRYLLVMKG APERILDRCS TILLQGKEQP LDEEMKEAFQ
NAYLELGGLG ERVLGFCHYY LPEEQFPKGF AFDCDDVNFT TDNLCFVGLM SMIDPPRAAV
PDAVGKCRSA GIKVIMVTGD HPITAKAIAK GVGIISEGNE TVEDIAARLN IPVSQVNPRD
AKACVIHGTD LKDFTSEQID EILQNHTEIV FARTSPQQKL IIVEGCQRQG AIVAVTGDGV
NDSPALKKAD IGVAMGIAGS DVSKQAADMI LLDDNFASIV TGVEEGRLIF DNLKKSIAYT
LTSNIPEITP FLLFIMANIP LPLGTITILC IDLGTDMVPA ISLAYEAAES DIMKRQPRNP
RTDKLVNERL ISMAYGQIGM IQALGGFFSY FVILAENGFL PGNLVGIRLN WDDRTVNDLE
DSYGQQWTYE QRKVVEFTCH TAFFVSIVVV QWADLIICKT RRNSVFQQGM KNKILIFGLF
EETALAAFLS YCPGMDVALR MYPLKPSWWF CAFPYSFLIF VYDEIRKLIL RRNPGGWVEK
ETYY*

speed

0.70 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems