mutation t@sting

Prediction

polymorphism

Model: simple_aae, prob: 0.00149485990609738 (classification due to TGP/ExAC, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
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)

chr3:150280445C>GN/A show variant in all transcripts IGV

HGNC symbol

EIF2A

Ensembl transcript ID

ENST00000460851

Genbank transcript ID

NM_032025

UniProt peptide

Q9BY44

alteration type

single base exchange

alteration region

CDS

DNA changes

c.290C>G
cDNA.399C>G
g.15981C>G

AA changes

T97S Score: 58 explain score(s)

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

frameshift

known variant

Reference ID: rs1132979

database	homozygous (G/G)	heterozygous	allele carriers
1000G	-	-	-
ExAC	7940	16887	24827

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.554	0.899
	3.848	1
(flanking)	1.044	1

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

splice sites

alteration within used splice site, likely to disturb normal splicing

effect	gDNA position	score	detection sequence	exon-intron border
Donor lost	15982	sequence motif lost	-	wt: ACTA\|gtaa mu: AGTA.gtaa
Donor marginally decreased	15982	wt: 0.9826 / mu: 0.9823 (marginal change - not scored)	wt: TACACTAGTAAGTAT mu: TACAGTAGTAAGTAT	CACT\|agta
Donor gained	15980	0.30	mu: CTTACAGTAGTAAGT	TACA\|gtag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

all conserved

Ptroglodytes

all identical

ENSPTRG00000015528

Mmulatta

all identical

ENSMMUG00000017696

119

Fcatus

all identical

ENSFCAG00000011331

120

Mmusculus

all identical

ENSMUSG00000027810

Ggallus

all conserved

ENSGALG00000010401

Trubripes

no homologue

Drerio

all identical

ENSDARG00000044479

Dmelanogaster

not conserved

FBgn0037135

104

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000020093

protein features

start (aa)	end (aa)	feature	details
125	163	REPEAT	WD 2.	might get lost (downstream of altered splice site)
150	150	CONFLICT	V -> A (in Ref. 4; AAQ13612).	might get lost (downstream of altered splice site)
173	173	CONFLICT	F -> S (in Ref. 4; AAQ13612).	might get lost (downstream of altered splice site)
261	261	CONFLICT	T -> P (in Ref. 1; AAM83402).	might get lost (downstream of altered splice site)
263	263	CONFLICT	G -> F (in Ref. 1; AAM83402).	might get lost (downstream of altered splice site)
268	268	CONFLICT	V -> L (in Ref. 1; AAM83402).	might get lost (downstream of altered splice site)
292	292	CONFLICT	Y -> S (in Ref. 1; AAM83402).	might get lost (downstream of altered splice site)
356	401	REPEAT	WD 3.	might get lost (downstream of altered splice site)
503	503	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
506	506	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
512	512	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
517	517	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
518	518	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
522	522	MOD_RES	Phosphothreonine.	might get lost (downstream of altered splice site)
531	582	COILED	Potential.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1758 / 1758

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

586 / 586

position of stopcodon in wt / mu cDNA

1867 / 1867

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

110 / 110

chromosome

strand

last intron/exon boundary

1802

theoretical NMD boundary in CDS

1642

length of CDS

1758

coding sequence (CDS) position

290

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

399

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

15981

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

150280445

original gDNA sequence snippet

GGCAACGTGGCAGCCTTACACTAGTAAGTATTTTCTCAGTG

altered gDNA sequence snippet

GGCAACGTGGCAGCCTTACAGTAGTAAGTATTTTCTCAGTG

original cDNA sequence snippet

GGCAACGTGGCAGCCTTACACTACTTCTAAAGATGGCACAG

altered cDNA sequence snippet

GGCAACGTGGCAGCCTTACAGTACTTCTAAAGATGGCACAG

wildtype AA sequence

MAPSTPLLTV RGSEGLYMVN GPPHFTESTV FPRESGKNCK VCIFSKDGTL FAWGNGEKVN
IISVTNKGLL HSFDLLKAVC LEFSPKNTVL ATWQPYTTSK DGTAGIPNLQ LYDVKTGTCL
KSFIQKKMQN WCPSWSEDET LCARNVNNEV HFFENNNFNT IANKLHLQKI NDFVLSPGPQ
PYKVAVYVPG SKGAPSFVRL YQYPNFAGPH AALANKSFFK ADKVTMLWNK KATAVLVIAS
TDVDKTGASY YGEQTLHYIA TNGESAVVQL PKNGPIYDVV WNSSSTEFCA VYGFMPAKAT
IFNLKCDPVF DFGTGPRNAA YYSPHGHILV LAGFGNLRGQ MEVWDVKNYK LISKPVASDS
TYFAWCPDGE HILTATCAPR LRVNNGYKIW HYTGSILHKY DVPSNAELWQ VSWQPFLDGI
FPAKTITYQA VPSEVPNEEP KVATAYRPPA LRNKPITNSK LHEEEPPQNM KPQSGNDKPL
SKTALKNQRK HEAKKAAKQE ARSDKSPDLA PTPAPQSTPR NTVSQSISGD PEIDKKIKNL
KKKLKAIEQL KEQAATGKQL EKNQLEKIQK ETALLQELED LELGI*

mutated AA sequence

MAPSTPLLTV RGSEGLYMVN GPPHFTESTV FPRESGKNCK VCIFSKDGTL FAWGNGEKVN
IISVTNKGLL HSFDLLKAVC LEFSPKNTVL ATWQPYSTSK DGTAGIPNLQ LYDVKTGTCL
KSFIQKKMQN WCPSWSEDET LCARNVNNEV HFFENNNFNT IANKLHLQKI NDFVLSPGPQ
PYKVAVYVPG SKGAPSFVRL YQYPNFAGPH AALANKSFFK ADKVTMLWNK KATAVLVIAS
TDVDKTGASY YGEQTLHYIA TNGESAVVQL PKNGPIYDVV WNSSSTEFCA VYGFMPAKAT
IFNLKCDPVF DFGTGPRNAA YYSPHGHILV LAGFGNLRGQ MEVWDVKNYK LISKPVASDS
TYFAWCPDGE HILTATCAPR LRVNNGYKIW HYTGSILHKY DVPSNAELWQ VSWQPFLDGI
FPAKTITYQA VPSEVPNEEP KVATAYRPPA LRNKPITNSK LHEEEPPQNM KPQSGNDKPL
SKTALKNQRK HEAKKAAKQE ARSDKSPDLA PTPAPQSTPR NTVSQSISGD PEIDKKIKNL
KKKLKAIEQL KEQAATGKQL EKNQLEKIQK ETALLQELED LELGI*

speed

1.10 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