MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 2 transcript(s)...
Querying Taster for transcript #1: ENST00000273783
Querying Taster for transcript #2: ENST00000444495
MT speed 0 s - this script 3.634202 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
EIF2B5	disease_causing_automatic	0.999995674143562	simple_aae		affected	0	V309L	single base exchange	rs113994061		show file
EIF2B5	disease_causing_automatic	0.999995674143562	simple_aae		affected	0	V309L	single base exchange	rs113994061		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999995674143562 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM023733)
known disease mutation: rs5947 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:183858287G>CN/A show variant in all transcripts IGV

HGNC symbol

EIF2B5

Ensembl transcript ID

ENST00000273783

Genbank transcript ID

NM_003907

UniProt peptide

Q13144

alteration type

single base exchange

alteration region

CDS

DNA changes

c.925G>C
cDNA.1047G>C
g.5462G>C

AA changes

V309L Score: 32 explain score(s)

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

309

frameshift

known variant

Reference ID: rs113994061

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	3	3

known disease mutation: rs5947 (pathogenic for Leukoencephalopathy with vanishing white matter) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM023733)

known disease mutation at this position, please check HGMD for details (HGMD ID CM023733)
known disease mutation at this position, please check HGMD for details (HGMD ID CM023733)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.85	0.589
	2.735	0.996
(flanking)	5.152	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
Acc increased	5471	wt: 0.27 / mu: 0.58	wt: TGTACTCAGCTGTCTGTGCTGACGTCATCCGCCGATGGGTC mu: TGTACTCAGCTCTCTGTGCTGACGTCATCCGCCGATGGGTC	gctg\|ACGT
Acc increased	5465	wt: 0.29 / mu: 0.39	wt: TACACATGTACTCAGCTGTCTGTGCTGACGTCATCCGCCGA mu: TACACATGTACTCAGCTCTCTGTGCTGACGTCATCCGCCGA	gtct\|GTGC
Acc gained	5467	0.70	mu: CACATGTACTCAGCTCTCTGTGCTGACGTCATCCGCCGATG	ctgt\|GCTG
Acc gained	5469	0.62	mu: CATGTACTCAGCTCTCTGTGCTGACGTCATCCGCCGATGGG	gtgc\|TGAC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

309

mutated

all conserved

309

Ptroglodytes

all identical

ENSPTRG00000015679

309

Mmulatta

all identical

ENSMMUG00000006562

309

Fcatus

all identical

ENSFCAG00000007787

309

Mmusculus

all identical

ENSMUSG00000003235

305

Ggallus

all identical

ENSGALG00000008376

295

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000074995

291

Dmelanogaster

all identical

FBgn0023512

275

Celegans

all conserved

D2085.3

273

Xtropicalis

all identical

ENSXETG00000014293

305

protein features

start (aa)	end (aa)	feature	details
505	509	COMPBIAS	Poly-Glu.	might get lost (downstream of altered splice site)
525	525	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
527	527	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
529	529	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
532	532	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
535	535	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
540	540	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
543	720	DOMAIN	W2.	might get lost (downstream of altered splice site)
544	544	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
547	567	HELIX		might get lost (downstream of altered splice site)
571	584	HELIX		might get lost (downstream of altered splice site)
589	602	HELIX		might get lost (downstream of altered splice site)
603	607	HELIX		might get lost (downstream of altered splice site)
614	635	HELIX		might get lost (downstream of altered splice site)
639	655	HELIX		might get lost (downstream of altered splice site)
657	662	HELIX		might get lost (downstream of altered splice site)
663	672	HELIX		might get lost (downstream of altered splice site)
678	685	HELIX		might get lost (downstream of altered splice site)
693	697	HELIX		might get lost (downstream of altered splice site)
701	714	HELIX		might get lost (downstream of altered splice site)
717	717	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
718	718	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2166 / 2166

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

722 / 722

position of stopcodon in wt / mu cDNA

2288 / 2288

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

123 / 123

chromosome

strand

last intron/exon boundary

2229

theoretical NMD boundary in CDS

2056

length of CDS

2166

coding sequence (CDS) position

925

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

1047

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

5462

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

183858287

original gDNA sequence snippet

ACCTACACATGTACTCAGCTGTCTGTGCTGACGTCATCCGC

altered gDNA sequence snippet

ACCTACACATGTACTCAGCTCTCTGTGCTGACGTCATCCGC

original cDNA sequence snippet

ACCTACACATGTACTCAGCTGTCTGTGCTGACGTCATCCGC

altered cDNA sequence snippet

ACCTACACATGTACTCAGCTCTCTGTGCTGACGTCATCCGC

wildtype AA sequence

MAAPVVAPPG VVVSRANKRS GAGPGGSGGG GARGAEEEPP PPLQAVLVAD SFDRRFFPIS
KDQPRVLLPL ANVALIDYTL EFLTATGVQE TFVFCCWKAA QIKEHLLKSK WCRPTSLNVV
RIITSELYRS LGDVLRDVDA KALVRSDFLL VYGDVISNIN ITRALEEHRL RRKLEKNVSV
MTMIFKESSP SHPTRCHEDN VVVAVDSTTN RVLHFQKTQG LRRFAFPLSL FQGSSDGVEV
RYDLLDCHIS ICSPQVAQLF TDNFDYQTRD DFVRGLLVNE EILGNQIHMH VTAKEYGARV
SNLHMYSAVC ADVIRRWVYP LTPEANFTDS TTQSCTHSRH NIYRGPEVSL GHGSILEENV
LLGSGTVIGS NCFITNSVIG PGCHIGDNVV LDQTYLWQGV RVAAGAQIHQ SLLCDNAEVK
ERVTLKPRSV LTSQVVVGPN ITLPEGSVIS LHPPDAEEDE DDGEFSDDSG ADQEKDKVKM
KGYNPAEVGA AGKGYLWKAA GMNMEEEEEL QQNLWGLKIN MEEESESESE QSMDSEEPDS
RGGSPQMDDI KVFQNEVLGT LQRGKEENIS CDNLVLEINS LKYAYNISLK EVMQVLSHVV
LEFPLQQMDS PLDSSRYCAL LLPLLKAWSP VFRNYIKRAA DHLEALAAIE DFFLEHEALG
ISMAKVLMAF YQLEILAEET ILSWFSQRDT TDKGQQLRKN QQLQRFIQWL KEAEEESSED
D*

mutated AA sequence

MAAPVVAPPG VVVSRANKRS GAGPGGSGGG GARGAEEEPP PPLQAVLVAD SFDRRFFPIS
KDQPRVLLPL ANVALIDYTL EFLTATGVQE TFVFCCWKAA QIKEHLLKSK WCRPTSLNVV
RIITSELYRS LGDVLRDVDA KALVRSDFLL VYGDVISNIN ITRALEEHRL RRKLEKNVSV
MTMIFKESSP SHPTRCHEDN VVVAVDSTTN RVLHFQKTQG LRRFAFPLSL FQGSSDGVEV
RYDLLDCHIS ICSPQVAQLF TDNFDYQTRD DFVRGLLVNE EILGNQIHMH VTAKEYGARV
SNLHMYSALC ADVIRRWVYP LTPEANFTDS TTQSCTHSRH NIYRGPEVSL GHGSILEENV
LLGSGTVIGS NCFITNSVIG PGCHIGDNVV LDQTYLWQGV RVAAGAQIHQ SLLCDNAEVK
ERVTLKPRSV LTSQVVVGPN ITLPEGSVIS LHPPDAEEDE DDGEFSDDSG ADQEKDKVKM
KGYNPAEVGA AGKGYLWKAA GMNMEEEEEL QQNLWGLKIN MEEESESESE QSMDSEEPDS
RGGSPQMDDI KVFQNEVLGT LQRGKEENIS CDNLVLEINS LKYAYNISLK EVMQVLSHVV
LEFPLQQMDS PLDSSRYCAL LLPLLKAWSP VFRNYIKRAA DHLEALAAIE DFFLEHEALG
ISMAKVLMAF YQLEILAEET ILSWFSQRDT TDKGQQLRKN QQLQRFIQWL KEAEEESSED
D*

speed

0.39 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

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999995674143562 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM023733)
known disease mutation: rs5947 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:183858287G>CN/A show variant in all transcripts IGV

HGNC symbol

EIF2B5

Ensembl transcript ID

ENST00000444495

Genbank transcript ID

N/A

UniProt peptide

Q13144

alteration type

single base exchange

alteration region

CDS

DNA changes

c.925G>C
cDNA.935G>C
g.5462G>C

AA changes

V309L Score: 32 explain score(s)

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

309

frameshift

known variant

Reference ID: rs113994061

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	3	3

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.85	0.589
	2.735	0.996
(flanking)	5.152	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
Acc increased	5471	wt: 0.27 / mu: 0.58	wt: TGTACTCAGCTGTCTGTGCTGACGTCATCCGCCGATGGGTC mu: TGTACTCAGCTCTCTGTGCTGACGTCATCCGCCGATGGGTC	gctg\|ACGT
Acc increased	5465	wt: 0.29 / mu: 0.39	wt: TACACATGTACTCAGCTGTCTGTGCTGACGTCATCCGCCGA mu: TACACATGTACTCAGCTCTCTGTGCTGACGTCATCCGCCGA	gtct\|GTGC
Acc gained	5467	0.70	mu: CACATGTACTCAGCTCTCTGTGCTGACGTCATCCGCCGATG	ctgt\|GCTG
Acc gained	5469	0.62	mu: CATGTACTCAGCTCTCTGTGCTGACGTCATCCGCCGATGGG	gtgc\|TGAC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

309

mutated

all conserved

309

Ptroglodytes

all identical

ENSPTRG00000015679

309

Mmulatta

all identical

ENSMMUG00000006562

309

Fcatus

all identical

ENSFCAG00000007787

309

Mmusculus

all identical

ENSMUSG00000003235

305

Ggallus

all identical

ENSGALG00000008376

295

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000074995

291

Dmelanogaster

all identical

FBgn0023512

275

Celegans

all conserved

D2085.3

273

Xtropicalis

all identical

ENSXETG00000014293

305

protein features

start (aa)	end (aa)	feature	details
505	509	COMPBIAS	Poly-Glu.	might get lost (downstream of altered splice site)
525	525	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
527	527	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
529	529	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
532	532	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
535	535	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
540	540	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
543	720	DOMAIN	W2.	might get lost (downstream of altered splice site)
544	544	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
547	567	HELIX		might get lost (downstream of altered splice site)
571	584	HELIX		might get lost (downstream of altered splice site)
589	602	HELIX		might get lost (downstream of altered splice site)
603	607	HELIX		might get lost (downstream of altered splice site)
614	635	HELIX		might get lost (downstream of altered splice site)
639	655	HELIX		might get lost (downstream of altered splice site)
657	662	HELIX		might get lost (downstream of altered splice site)
663	672	HELIX		might get lost (downstream of altered splice site)
678	685	HELIX		might get lost (downstream of altered splice site)
693	697	HELIX		might get lost (downstream of altered splice site)
701	714	HELIX		might get lost (downstream of altered splice site)
717	717	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)
718	718	MOD_RES	Phosphoserine.	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

2118 / 2118

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

706 / 706

position of stopcodon in wt / mu cDNA

2128 / 2128

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

11 / 11

chromosome

strand

last intron/exon boundary

2117

theoretical NMD boundary in CDS

2056

length of CDS

2118

coding sequence (CDS) position

925

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

935

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

5462

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

183858287

original gDNA sequence snippet

ACCTACACATGTACTCAGCTGTCTGTGCTGACGTCATCCGC

altered gDNA sequence snippet

ACCTACACATGTACTCAGCTCTCTGTGCTGACGTCATCCGC

original cDNA sequence snippet

ACCTACACATGTACTCAGCTGTCTGTGCTGACGTCATCCGC

altered cDNA sequence snippet

ACCTACACATGTACTCAGCTCTCTGTGCTGACGTCATCCGC

wildtype AA sequence

mutated AA sequence

MAAPVVAPPG VVVSRANKRS GAGPGGSGGG GARGAEEEPP PPLQAVLVAD SFDRRFFPIS
KDQPRVLLPL ANVALIDYTL EFLTATGVQE TFVFCCWKAA QIKEHLLKSK WCRPTSLNVV
RIITSELYRS LGDVLRDVDA KALVRSDFLL VYGDVISNIN ITRALEEHRL RRKLEKNVSV
MTMIFKESSP SHPTRCHEDN VVVAVDSTTN RVLHFQKTQG LRRFAFPLSL FQGSSDGVEV
RYDLLDCHIS ICSPQVAQLF TDNFDYQTRD DFVRGLLVNE EILGNQIHMH VTAKEYGARV
SNLHMYSALC ADVIRRWVYP LTPEANFTDS TTQSCTHSRH NIYRGPEVSL GHGSILEENV
LLGSGTVIGS NCFITNSVIG PGCHIGDNVV LDQTYLWQGV RVAAGAQIHQ SLLCDNAEVK
ERVTLKPRSV LTSQVVVGPN ITLPEGSVIS LHPPDAEEDE DDGEFSDDSG ADQEKDKVKM
KGYNPAEVGA AGKGYLWKAA GMNMEEEEEL QQNLWGLKIN MEEESESESE QSMDSEEPDS
RGGSPQMDDI KVFQNEVLGT LQRGKEENIS CDNLVLEINS LKYAYNISLK EVMQVLSHVV
LEFPLQQMDS PLDSSRYCAL LLPLLKAWSP VFRNYIKRAA DHLEALAAIE DFFLEHEALG
ISMAKVLMAF YQLEILAEET ILSWFSQRDT TDKGQQLRKN QQVVC*

speed

1.24 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems