mutation t@sting

Prediction

polymorphism

Model: without_aae, prob: 8.51550170791688e-17 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

homozygous in TGP or ExAC
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:89521693T>CN/A show variant in all transcripts IGV

HGNC symbol

EPHA3

Ensembl transcript ID

ENST00000494014

Genbank transcript ID

N/A

UniProt peptide

P29320

alteration type

single base exchange

alteration region

intron

DNA changes

g.365020T>C

AA changes

N/A

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

N/A

frameshift

N/A

known variant

Reference ID: rs35124509

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	9366	14035	23401

regulatory features

N/A

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.54	0.988
	1.395	0.999
(flanking)	4.127	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 increased	365020	wt: 0.37 / mu: 0.72	wt: GTGTCTGGACAGCAC mu: GTGTCCGGACAGCAC	GTCT\|ggac
Donor increased	365011	wt: 0.45 / mu: 0.62	wt: GGCTTAATGGTGTCT mu: GGCTTAATGGTGTCC	CTTA\|atgg

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

N/A

protein features

start (aa)	end (aa)	feature	details
566	983	TOPO_DOM	Cytoplasmic (Potential).	might get lost (downstream of altered splice site)
911	975	DOMAIN	SAM.	might get lost (downstream of altered splice site)
937	937	MOD_RES	Phosphotyrosine (By similarity).	might get lost (downstream of altered splice site)
981	983	MOTIF	PDZ-binding (Potential).	might get lost (downstream of altered splice site)

length of protein

N/A

AA sequence altered

N/A

position of stopcodon in wt / mu CDS

N/A

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

N/A

position of stopcodon in wt / mu cDNA

N/A

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

74 / 74

chromosome

strand

last intron/exon boundary

2823

theoretical NMD boundary in CDS

2699

length of CDS

2757

coding sequence (CDS) position

N/A

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

N/A

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

365020

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

89521693

original gDNA sequence snippet

GTGACTGGCTTAATGGTGTCTGGACAGCACACTGCAAGGAA

altered gDNA sequence snippet

GTGACTGGCTTAATGGTGTCCGGACAGCACACTGCAAGGAA

original cDNA sequence snippet

N/A

altered cDNA sequence snippet

N/A

wildtype AA sequence

MDCQLSILLL LSCSVLDSFG ELIPQPSNEV NLLDSKTIQG ELGWISYPSH GWEEISGVDE
HYTPIRTYQV CNVMDHSQNN WLRTNWVPRN SAQKIYVELK FTLRDCNSIP LVLGTCKETF
NLYYMESDDD HGVKFREHQF TKIDTIAADE SFTQMDLGDR ILKLNTEIRE VGPVNKKGFY
LAFQDVGACV ALVSVRVYFK KCPFTVKNLA MFPDTVPMDS QSLVEVRGSC VNNSKEEDPP
RMYCSTEGEW LVPIGKCSCN AGYEERGFMC QACRPGFYKA LDGNMKCAKC PPHSSTQEDG
SMNCRCENNY FRADKDPPSM ACTRPPSSPR NVISNINETS VILDWSWPLD TGGRKDVTFN
IICKKCGWNI KQCEPCSPNV RFLPRQFGLT NTTVTVTDLL AHTNYTFEID AVNGVSELSS
PPRQFAAVSI TTNQAAPSPV LTIKKDRTSR NSISLSWQEP EHPNGIILDY EVKYYEKQEQ
ETSYTILRAR GTNVTISSLK PDTIYVFQIR ARTAAGYGTN SRKFEFETSP DSFSISGESS
QVVMIAISAA VAIILLTVVI YVLIGRFCGY KSKHGADEKR LHFGNGHLKL PGLRTYVDPH
TYEDPTQAVH EFAKELDATN ISIDKVVGAG EFGEVCSGRL KLPSKKEISV AIKTLKVGYT
EKQRRDFLGE ASIMGQFDHP NIIRLEGVVT KSKPVMIVTE YMENGSLDSF LRKHDAQFTV
IQLVGMLRGI ASGMKYLSDM GYVHRDLAAR NILINSNLVC KVSDFGLSRV LEDDPEAAYT
TRGGKIPIRW TSPEAIAYRK FTSASDVWSY GIVLWEVMSY GERPYWEMSN QDVIKAVDEG
YRLPPPMDCP AALYQLMLDC WQKDRNNRPK FEQIVSILDK LIRNPGSLKI ITSAAARPSN
LLLDQSNVDI TTFRTTVT*

mutated AA sequence

N/A

speed

0.78 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