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 2.789219 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
EPHA2	disease_causing	0.999989844560861	simple_aae				R721Q	single base exchange	rs116506614		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999989844560861 (explain)

Summary

amino acid sequence changed
heterozygous in TGP or ExAC
known disease mutation at this position (HGMD CM0910311)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:16458722C>TN/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.2162G>A
cDNA.2317G>A
g.23861G>A

AA changes

R721Q Score: 43 explain score(s)

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

721

frameshift

known variant

Reference ID: rs116506614

database	homozygous (T/T)	heterozygous	allele carriers
1000G	0	1	1
ExAC	0	72	72

known disease mutation at this position, please check HGMD for details (HGMD ID CM0910311)

known disease mutation at this position, please check HGMD for details (HGMD ID CM0910311)
known disease mutation at this position, please check HGMD for details (HGMD ID CM0910311)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Promoter Associated, Regulatory Feature, Promoter like regulatory feature

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.462	1
	3.103	1
(flanking)	0.343	0.999

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	23858	wt: 0.4505 / mu: 0.4948 (marginal change - not scored)	wt: CATGCTGCGGGGCAT mu: CATGCTGCAGGGCAT	TGCT\|gcgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

721

mutated

all conserved

721

Ptroglodytes

all identical

ENSPTRG00000000221

675

Mmulatta

all identical

ENSMMUG00000018245

719

Fcatus

all identical

ENSFCAG00000010170

691

Mmusculus

all identical

ENSMUSG00000006445

722

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000001093

730

Drerio

all identical

ENSDARG00000022727

723

Dmelanogaster

all identical

FBgn0025936

850

Celegans

no homologue

Xtropicalis

no alignment

ENSXETG00000021731

n/a

protein features

start (aa)	end (aa)	feature	details
559	976	TOPO_DOM	Cytoplasmic (Potential).	lost
606	906	REGION	Mediates interaction with ARHGEF16 and ELMO2.	lost
613	875	DOMAIN	Protein kinase.	lost
713	732	HELIX		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

2162

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

2317

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

23861

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

16458722

original gDNA sequence snippet

GCAGCTGGTGGGCATGCTGCGGGGCATCGCAGCTGGCATGA

altered gDNA sequence snippet

GCAGCTGGTGGGCATGCTGCAGGGCATCGCAGCTGGCATGA

original cDNA sequence snippet

GCAGCTGGTGGGCATGCTGCGGGGCATCGCAGCTGGCATGA

altered cDNA sequence snippet

GCAGCTGGTGGGCATGCTGCAGGGCATCGCAGCTGGCATGA

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

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
QGIAAGMKYL 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*

speed

0.73 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