MutationTaster - study a chromosomal position

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input seems to be ok - now mapping the variant to the different transcripts...
found 3 transcript(s)...
Querying Taster for transcript #1: ENST00000273783
Querying Taster for transcript #2: ENST00000432569
Querying Taster for transcript #3: ENST00000444495
MT speed 0 s - this script 4.922882 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
EIF2B5	polymorphism	0.039410346142981	simple_aae				A16D	single base exchange	rs113994041		show file
EIF2B5	polymorphism	0.039410346142981	simple_aae				A16D	single base exchange	rs113994041		show file
EIF2B5	polymorphism	0.039410346142981	simple_aae				A16D	single base exchange	rs113994041		show file

Taster files

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.960589653857019 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM041311)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:183853220C>AN/A show variant in all transcripts IGV

HGNC symbol

EIF2B5

Ensembl transcript ID

ENST00000432569

Genbank transcript ID

N/A

UniProt peptide

Q13144

alteration type

single base exchange

alteration region

CDS

DNA changes

c.47C>A
cDNA.68C>A
g.395C>A

AA changes

A16D Score: 126 explain score(s)

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

frameshift

known variant

Reference ID: rs113994041
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation at this position, please check HGMD for details (HGMD ID CM041311)

known disease mutation at this position, please check HGMD for details (HGMD ID CM041311)
known disease mutation at this position, please check HGMD for details (HGMD ID CM041311)

regulatory features

ETS1, Transcription Factor, ETS1 Transcription Factor Binding
H4K5ac, Histone, Histone 4 Lysine 5 Acetylation
ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
Max, Transcription Factor, Max TF binding
H2BK120ac, Histone, Histone 2B Lysine 120 Acetylation
Gabp, Transcription Factor, Gabp TF binding
POU2F2, Transcription Factor, POU2F2 Transcription Factor Binding
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
H2AZ, Histone, Histone 2A variant Z
SIX5, Transcription Factor, SIX5 Transcription Factor Binding
SP1, Transcription Factor, SP1 Transcription Factor Binding
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
E2F4, Transcription Factor, E2F4 Transcription Factor Binding
MOF, Transcription Factor, MOF Transcription Factor Binding
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Cmyc, Transcription Factor, Cmyc TF binding
H3K18ac, Histone, Histone 3 Lysine 18 Acetylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
Ap2gamma, Transcription Factor, Ap2gamma Transcription Factor Binding
H2BK20ac, Histone, Histone 2B Lysine 20 Acetylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
CTCF, Transcription Factor, CCCTC-binding factor
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
H2BK5ac, Histone, Histone 2B Lysine 5 Acetylation
Ap2alpha, Transcription Factor, Ap2alpha Transcription Factor Binding
CTCFL, Transcription Factor, CTCFL Transcription Factor Binding
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
H3K4ac, Histone, Histone 3 Lysine 4 Acetylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
PU1, Transcription Factor, PU1 Transcription Factor Binding

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.21	0.582
	0.455	0.404
(flanking)	-0.622	0.051

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 marginally increased	388	wt: 0.2219 / mu: 0.2247 (marginal change - not scored)	wt: CGCCGCCTGGTGTGGTGGTTAGTCGGGCTAACAAGCGCAGC mu: CGCCGCCTGGTGTGGTGGTTAGTCGGGATAACAAGCGCAGC	gtta\|GTCG
Donor marginally increased	398	wt: 0.6014 / mu: 0.6154 (marginal change - not scored)	wt: GGCTAACAAGCGCAG mu: GGATAACAAGCGCAG	CTAA\|caag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000015679

Mmulatta

all identical

ENSMMUG00000006562

Fcatus

all identical

ENSFCAG00000007787

Mmusculus

all identical

ENSMUSG00000003235

Ggallus

no alignment

ENSGALG00000008376

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000074995

n/a

Dmelanogaster

no alignment

FBgn0023512

n/a

Celegans

no alignment

D2085.3

n/a

Xtropicalis

all identical

ENSXETG00000014293

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

324 / 324

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

108 / 108

position of stopcodon in wt / mu cDNA

345 / 345

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

22 / 22

chromosome

strand

last intron/exon boundary

217

theoretical NMD boundary in CDS

145

length of CDS

324

coding sequence (CDS) position

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

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

395

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

183853220

original gDNA sequence snippet

TGGTGTGGTGGTTAGTCGGGCTAACAAGCGCAGCGGCGCGG

altered gDNA sequence snippet

TGGTGTGGTGGTTAGTCGGGATAACAAGCGCAGCGGCGCGG

original cDNA sequence snippet

TGGTGTGGTGGTTAGTCGGGCTAACAAGCGCAGCGGCGCGG

altered cDNA sequence snippet

TGGTGTGGTGGTTAGTCGGGATAACAAGCGCAGCGGCGCGG

wildtype AA sequence

MAAPVVAPPG VVVSRANKRS GAGPGGSGGG GARGAEEEPP PPLQAVLVAD SFDRRFFPIS
KDQPRVLLPL ANVALIDYTL EFLTATGVQE TFVFCCWKAA QIKEHLL*

mutated AA sequence

MAAPVVAPPG VVVSRDNKRS GAGPGGSGGG GARGAEEEPP PPLQAVLVAD SFDRRFFPIS
KDQPRVLLPL ANVALIDYTL EFLTATGVQE TFVFCCWKAA QIKEHLL*

speed

1.52 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

polymorphism

Model: simple_aae, prob: 0.960589653857019 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM041311)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:183853220C>AN/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.47C>A
cDNA.169C>A
g.395C>A

AA changes

A16D Score: 126 explain score(s)

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

frameshift

known variant

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.21	0.582
	0.455	0.404
(flanking)	-0.622	0.051

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 marginally increased	388	wt: 0.2219 / mu: 0.2247 (marginal change - not scored)	wt: CGCCGCCTGGTGTGGTGGTTAGTCGGGCTAACAAGCGCAGC mu: CGCCGCCTGGTGTGGTGGTTAGTCGGGATAACAAGCGCAGC	gtta\|GTCG
Donor marginally increased	398	wt: 0.6014 / mu: 0.6154 (marginal change - not scored)	wt: GGCTAACAAGCGCAG mu: GGATAACAAGCGCAG	CTAA\|caag

distance from splice site

149

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000015679

Mmulatta

all identical

ENSMMUG00000006562

Fcatus

all identical

ENSFCAG00000007787

Mmusculus

all identical

ENSMUSG00000003235

Ggallus

no alignment

ENSGALG00000008376

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000074995

n/a

Dmelanogaster

no alignment

FBgn0023512

n/a

Celegans

no alignment

D2085.3

n/a

Xtropicalis

all identical

ENSXETG00000014293

protein features

no protein features affected

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

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

169

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

395

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

183853220

original gDNA sequence snippet

TGGTGTGGTGGTTAGTCGGGCTAACAAGCGCAGCGGCGCGG

altered gDNA sequence snippet

TGGTGTGGTGGTTAGTCGGGATAACAAGCGCAGCGGCGCGG

original cDNA sequence snippet

TGGTGTGGTGGTTAGTCGGGCTAACAAGCGCAGCGGCGCGG

altered cDNA sequence snippet

TGGTGTGGTGGTTAGTCGGGATAACAAGCGCAGCGGCGCGG

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 VVVSRDNKRS 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*

speed

1.45 s

mutation t@sting

documentation

Prediction

polymorphism

Model: simple_aae, prob: 0.960589653857019 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM041311)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:183853220C>AN/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.47C>A
cDNA.57C>A
g.395C>A

AA changes

A16D Score: 126 explain score(s)

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

frameshift

known variant

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.21	0.582
	0.455	0.404
(flanking)	-0.622	0.051

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 marginally increased	388	wt: 0.2219 / mu: 0.2247 (marginal change - not scored)	wt: CGCCGCCTGGTGTGGTGGTTAGTCGGGCTAACAAGCGCAGC mu: CGCCGCCTGGTGTGGTGGTTAGTCGGGATAACAAGCGCAGC	gtta\|GTCG
Donor marginally increased	398	wt: 0.6014 / mu: 0.6154 (marginal change - not scored)	wt: GGCTAACAAGCGCAG mu: GGATAACAAGCGCAG	CTAA\|caag

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

mutated

not conserved

Ptroglodytes

all identical

ENSPTRG00000015679

Mmulatta

all identical

ENSMMUG00000006562

Fcatus

all identical

ENSFCAG00000007787

Mmusculus

all identical

ENSMUSG00000003235

Ggallus

no alignment

ENSGALG00000008376

n/a

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000074995

n/a

Dmelanogaster

no alignment

FBgn0023512

n/a

Celegans

no alignment

D2085.3

n/a

Xtropicalis

all identical

ENSXETG00000014293

protein features

no protein features affected

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

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

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

395

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

183853220

original gDNA sequence snippet

TGGTGTGGTGGTTAGTCGGGCTAACAAGCGCAGCGGCGCGG

altered gDNA sequence snippet

TGGTGTGGTGGTTAGTCGGGATAACAAGCGCAGCGGCGCGG

original cDNA sequence snippet

TGGTGTGGTGGTTAGTCGGGCTAACAAGCGCAGCGGCGCGG

altered cDNA sequence snippet

TGGTGTGGTGGTTAGTCGGGATAACAAGCGCAGCGGCGCGG

wildtype AA sequence

mutated AA sequence

speed

1.37 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

mutation t@sting

Prediction

polymorphism

Problems