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 2.930069 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
EPM2A	disease_causing_automatic	0.999999999819642	simple_aae			0	R108C	single base exchange	rs137852915		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999819642 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM980606)
known disease mutation: rs3100 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr6:146007412G>AN/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.322C>T
cDNA.848C>T
g.49749C>T

AA changes

R108C Score: 180 explain score(s)

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

108

frameshift

known variant

Reference ID: rs137852915

database	homozygous (A/A)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	4	4

known disease mutation: rs3100 (pathogenic for Lafora disease) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980606)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980606)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980606)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.828	1
	4.099	1
(flanking)	0.388	0.999

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

108

mutated

not conserved

108

Ptroglodytes

all identical

ENSPTRG00000018681

108

Mmulatta

all identical

ENSMMUG00000010643

108

Fcatus

all identical

ENSFCAG00000011712

Mmusculus

all identical

ENSMUSG00000055493

108

Ggallus

all identical

ENSGALG00000012275

105

Trubripes

no homologue

Drerio

all identical

ENSDARG00000059044

102

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000017691

101

protein features

start (aa)	end (aa)	feature	details
1	124	DOMAIN	CBM20.	lost

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

322

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

848

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

49749

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

146007412

original gDNA sequence snippet

GCAATGGACCTCATCATGACCGTTGCTGTACTTACAATGAA

altered gDNA sequence snippet

GCAATGGACCTCATCATGACTGTTGCTGTACTTACAATGAA

original cDNA sequence snippet

GCAATGGACCTCATCATGACCGTTGCTGTACTTACAATGAA

altered cDNA sequence snippet

GCAATGGACCTCATCATGACTGTTGCTGTACTTACAATGAA

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 GNGPHHDCCC TYNENNLVDG
VYCLPIGHWI EATGHTNEMK HTTDFYFNIA GHQAMHYSRI LPNIWLGSCP RQVEHVTIKL
KHELGITAVM NFQTEWDIVQ NSSGCNRYPE PMTPDTMIKL YREEGLAYIW MPTPDMSTEG
RVQMLPQAVC LLHALLEKGH IVYVHCNAGV GRSTAAVCGW LQYVMGWNLR KVQYFLMAKR
PAVYIDEEAL ARAQEDFFQK FGKVRSSVCS L*

speed

0.92 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