MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 1 transcript(s)...
Querying Taster for transcript #1: ENST00000367519
MT speed 0 s - this script 3.016912 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
EPM2A	disease_causing_automatic	0.999999999036014	simple_aae		affected	0	G279S	single base exchange	rs137852917		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999036014 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM149989)
known disease mutation at this position (HGMD CM980609)
known disease mutation: rs3099 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:145948713C>TN/A show variant in all transcripts IGV

HGNC symbol

EPM2A

Ensembl transcript ID

ENST00000367519

Genbank transcript ID

NM_005670

UniProt peptide

O95278

alteration type

single base exchange

alteration region

CDS

DNA changes

c.835G>A
cDNA.1361G>A
g.108448G>A

AA changes

G279S Score: 56 explain score(s)

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

279

frameshift

known variant

Reference ID: rs137852917
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs3099 (pathogenic for Lafora disease|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980609)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980609)
known disease mutation at this position, please check HGMD for details (HGMD ID CM149989)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980609)
known disease mutation at this position, please check HGMD for details (HGMD ID CM149989)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980609)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.774	1
	5.774	1
(flanking)	-0.624	0.571

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	108449	wt: 0.3384 / mu: 0.3503 (marginal change - not scored)	wt: CTCCACCGCGGCTGTCTGCGGCTGGCTCCAGTATGTGATGG mu: CTCCACCGCGGCTGTCTGCAGCTGGCTCCAGTATGTGATGG	gcgg\|CTGG
Acc increased	108445	wt: 0.33 / mu: 0.38	wt: GCCGCTCCACCGCGGCTGTCTGCGGCTGGCTCCAGTATGTG mu: GCCGCTCCACCGCGGCTGTCTGCAGCTGGCTCCAGTATGTG	gtct\|GCGG
Donor gained	108448	0.32	mu: TCTGCAGCTGGCTCC	TGCA\|gctg

distance from splice site

117

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

279

mutated

not conserved

279

Ptroglodytes

all identical

ENSPTRG00000018681

279

Mmulatta

all identical

ENSMMUG00000010643

279

Fcatus

all identical

ENSFCAG00000011712

178

Mmusculus

all identical

ENSMUSG00000055493

278

Ggallus

all identical

ENSGALG00000012275

266

Trubripes

no homologue

Drerio

all identical

ENSDARG00000059044

263

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000017691

261

protein features

start (aa)	end (aa)	feature	details
243	311	DOMAIN	Tyrosine-protein phosphatase.	lost
294	294	CONFLICT	Y -> H (in Ref. 5; BAG61454).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

996 / 996

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

332 / 332

position of stopcodon in wt / mu cDNA

1522 / 1522

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

527 / 527

chromosome

strand

-1

last intron/exon boundary

1245

theoretical NMD boundary in CDS

668

length of CDS

996

coding sequence (CDS) position

835

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

1361

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

108448

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

145948713

original gDNA sequence snippet

GCTCCACCGCGGCTGTCTGCGGCTGGCTCCAGTATGTGATG

altered gDNA sequence snippet

GCTCCACCGCGGCTGTCTGCAGCTGGCTCCAGTATGTGATG

original cDNA sequence snippet

GCTCCACCGCGGCTGTCTGCGGCTGGCTCCAGTATGTGATG

altered cDNA sequence snippet

GCTCCACCGCGGCTGTCTGCAGCTGGCTCCAGTATGTGATG

wildtype AA sequence

MRFRFGVVVP PAVAGARPEL LVVGSRPELG RWEPRGAVRL RPAGTAAGDG ALALQEPGLW
LGEVELAAEE AAQDGAEPGR VDTFWYKFLK REPGGELSWE GNGPHHDRCC TYNENNLVDG
VYCLPIGHWI EATGHTNEMK HTTDFYFNIA GHQAMHYSRI LPNIWLGSCP RQVEHVTIKL
KHELGITAVM NFQTEWDIVQ NSSGCNRYPE PMTPDTMIKL YREEGLAYIW MPTPDMSTEG
RVQMLPQAVC LLHALLEKGH IVYVHCNAGV GRSTAAVCGW LQYVMGWNLR KVQYFLMAKR
PAVYIDEEAL ARAQEDFFQK FGKVRSSVCS L*

mutated AA sequence

MRFRFGVVVP PAVAGARPEL LVVGSRPELG RWEPRGAVRL RPAGTAAGDG ALALQEPGLW
LGEVELAAEE AAQDGAEPGR VDTFWYKFLK REPGGELSWE GNGPHHDRCC TYNENNLVDG
VYCLPIGHWI EATGHTNEMK HTTDFYFNIA GHQAMHYSRI LPNIWLGSCP RQVEHVTIKL
KHELGITAVM NFQTEWDIVQ NSSGCNRYPE PMTPDTMIKL YREEGLAYIW MPTPDMSTEG
RVQMLPQAVC LLHALLEKGH IVYVHCNAGV GRSTAAVCSW LQYVMGWNLR KVQYFLMAKR
PAVYIDEEAL ARAQEDFFQK FGKVRSSVCS L*

speed

0.95 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

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

Problems