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: ENST00000358432
MT speed 0 s - this script 2.680824 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
EPHA2	disease_causing_automatic	0.938860132533208	simple_aae			0	T940I	single base exchange	rs137853200		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.938860132533208 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM092928)
known disease mutation: rs13259 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:16455935G>AN/A show variant in all transcripts IGV

HGNC symbol

EPHA2

Ensembl transcript ID

ENST00000358432

Genbank transcript ID

NM_004431

UniProt peptide

P29317

alteration type

single base exchange

alteration region

CDS

DNA changes

c.2819C>T
cDNA.2974C>T
g.26648C>T

AA changes

T940I Score: 89 explain score(s)

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

940

frameshift

known variant

Reference ID: rs137853200
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs13259 (pathogenic for Cataract 6, multiple types) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM092928)

known disease mutation at this position, please check HGMD for details (HGMD ID CM092928)
known disease mutation at this position, please check HGMD for details (HGMD ID CM092928)

regulatory features

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

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	1.797	1
	2.554	1
(flanking)	3.293	1

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 marginally increased	26653	wt: 0.9868 / mu: 0.9904 (marginal change - not scored)	wt: CCAACGAGTAAGTCA mu: TCAACGAGTAAGTCA	AACG\|agta

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

940

mutated

not conserved

940

Ptroglodytes

all identical

ENSPTRG00000000221

894

Mmulatta

all identical

ENSMMUG00000018245

938

Fcatus

all identical

ENSFCAG00000010170

910

Mmusculus

all conserved

ENSMUSG00000006445

941

Ggallus

no homologue

Trubripes

not conserved

ENSTRUG00000001093

949

Drerio

not conserved

ENSDARG00000022727

942

Dmelanogaster

all identical

FBgn0025936

1068

Celegans

no homologue

Xtropicalis

not conserved

ENSXETG00000021731

746

protein features

start (aa)	end (aa)	feature	details
559	976	TOPO_DOM	Cytoplasmic (Potential).	lost
886	976	REGION	Negatively regulates interaction with ARHGEF16.	lost
904	968	DOMAIN	SAM.	lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2931 / 2931

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

977 / 977

position of stopcodon in wt / mu cDNA

3086 / 3086

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

156 / 156

chromosome

strand

-1

last intron/exon boundary

2981

theoretical NMD boundary in CDS

2775

length of CDS

2931

coding sequence (CDS) position

2819

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

2974

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

26648

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

16455935

original gDNA sequence snippet

CGAGAAGGTGGTGCAGATGACCAACGAGTAAGTCAGGCCCC

altered gDNA sequence snippet

CGAGAAGGTGGTGCAGATGATCAACGAGTAAGTCAGGCCCC

original cDNA sequence snippet

CGAGAAGGTGGTGCAGATGACCAACGACGACATCAAGAGGA

altered cDNA sequence snippet

CGAGAAGGTGGTGCAGATGATCAACGACGACATCAAGAGGA

wildtype AA sequence

MELQAARACF ALLWGCALAA AAAAQGKEVV LLDFAAAGGE LGWLTHPYGK GWDLMQNIMN
DMPIYMYSVC NVMSGDQDNW LRTNWVYRGE AERIFIELKF TVRDCNSFPG GASSCKETFN
LYYAESDLDY GTNFQKRLFT KIDTIAPDEI TVSSDFEARH VKLNVEERSV GPLTRKGFYL
AFQDIGACVA LLSVRVYYKK CPELLQGLAH FPETIAGSDA PSLATVAGTC VDHAVVPPGG
EEPRMHCAVD GEWLVPIGQC LCQAGYEKVE DACQACSPGF FKFEASESPC LECPEHTLPS
PEGATSCECE EGFFRAPQDP ASMPCTRPPS APHYLTAVGM GAKVELRWTP PQDSGGREDI
VYSVTCEQCW PESGECGPCE ASVRYSEPPH GLTRTSVTVS DLEPHMNYTF TVEARNGVSG
LVTSRSFRTA SVSINQTEPP KVRLEGRSTT SLSVSWSIPP PQQSRVWKYE VTYRKKGDSN
SYNVRRTEGF SVTLDDLAPD TTYLVQVQAL TQEGQGAGSK VHEFQTLSPE GSGNLAVIGG
VAVGVVLLLV LAGVGFFIHR RRKNQRARQS PEDVYFSKSE QLKPLKTYVD PHTYEDPNQA
VLKFTTEIHP SCVTRQKVIG AGEFGEVYKG MLKTSSGKKE VPVAIKTLKA GYTEKQRVDF
LGEAGIMGQF SHHNIIRLEG VISKYKPMMI ITEYMENGAL DKFLREKDGE FSVLQLVGML
RGIAAGMKYL ANMNYVHRDL AARNILVNSN LVCKVSDFGL SRVLEDDPEA TYTTSGGKIP
IRWTAPEAIS YRKFTSASDV WSFGIVMWEV MTYGERPYWE LSNHEVMKAI NDGFRLPTPM
DCPSAIYQLM MQCWQQERAR RPKFADIVSI LDKLIRAPDS LKTLADFDPR VSIRLPSTSG
SEGVPFRTVS EWLESIKMQQ YTEHFMAAGY TAIEKVVQMT NDDIKRIGVR LPGHQKRIAY
SLLGLKDQVN TVGIPI*

mutated AA sequence

speed

0.68 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