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 2.508368 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
EIF2B5	disease_causing	0.999998504522557	simple_aae				L68S	single base exchange	rs113994044		show file
EIF2B5	disease_causing	0.999998504522557	simple_aae				L68S	single base exchange	rs113994044		show file
EIF2B5	disease_causing	0.999998504522557	simple_aae				L68S	single base exchange	rs113994044		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999998504522557 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM051468)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:183854407T>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.203T>C
cDNA.325T>C
g.1582T>C

AA changes

L68S Score: 145 explain score(s)

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

frameshift

known variant

Reference ID: rs113994044

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

known disease mutation at this position, please check HGMD for details (HGMD ID CM051468)

known disease mutation at this position, please check HGMD for details (HGMD ID CM051468)
known disease mutation at this position, please check HGMD for details (HGMD ID CM051468)

regulatory features

H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H3K9me1, Histone, Histone 3 Lysine 9 mono-methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
H3K79me2, Histone, Histone 3 Lysine 79 di-methylation
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
H3K23ac, Histone, Histone 3 Lysine 23 Acetylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.041	0.991
	4.987	1
(flanking)	0.435	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 marginally increased	1573	wt: 0.9319 / mu: 0.9350 (marginal change - not scored)	wt: TTTTTCATCTTGTATCCTTCAGGTCCTCTTGCCCCTGGCCA mu: TTTTTCATCTTGTATCCTTCAGGTCCTCTCGCCCCTGGCCA	ttca\|GGTC
Acc marginally increased	1583	wt: 0.3592 / mu: 0.3749 (marginal change - not scored)	wt: TGTATCCTTCAGGTCCTCTTGCCCCTGGCCAATGTGGCATT mu: TGTATCCTTCAGGTCCTCTCGCCCCTGGCCAATGTGGCATT	cttg\|CCCC
Acc marginally increased	1586	wt: 0.2446 / mu: 0.2672 (marginal change - not scored)	wt: ATCCTTCAGGTCCTCTTGCCCCTGGCCAATGTGGCATTAAT mu: ATCCTTCAGGTCCTCTCGCCCCTGGCCAATGTGGCATTAAT	gccc\|CTGG
Acc marginally increased	1588	wt: 0.8656 / mu: 0.8684 (marginal change - not scored)	wt: CCTTCAGGTCCTCTTGCCCCTGGCCAATGTGGCATTAATTG mu: CCTTCAGGTCCTCTCGCCCCTGGCCAATGTGGCATTAATTG	ccct\|GGCC

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

all identical

ENSGALG00000008376

Trubripes

no homologue

Drerio

all identical

ENSDARG00000074995

Dmelanogaster

all identical

FBgn0023512

Celegans

all conserved

D2085.3

Xtropicalis

all conserved

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

203

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

325

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

1582

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

183854407

original gDNA sequence snippet

TTGTATCCTTCAGGTCCTCTTGCCCCTGGCCAATGTGGCAT

altered gDNA sequence snippet

TTGTATCCTTCAGGTCCTCTCGCCCCTGGCCAATGTGGCAT

original cDNA sequence snippet

GGACCAGCCTCGGGTCCTCTTGCCCCTGGCCAATGTGGCAT

altered cDNA sequence snippet

GGACCAGCCTCGGGTCCTCTCGCCCCTGGCCAATGTGGCAT

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
KDQPRVLSPL 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

0.28 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: 0.999998504522557 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM051468)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:183854407T>CN/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.203T>C
cDNA.224T>C
g.1582T>C

AA changes

L68S Score: 145 explain score(s)

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

frameshift

known variant

Reference ID: rs113994044

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.041	0.991
	4.987	1
(flanking)	0.435	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 marginally increased	1573	wt: 0.9319 / mu: 0.9350 (marginal change - not scored)	wt: TTTTTCATCTTGTATCCTTCAGGTCCTCTTGCCCCTGGCCA mu: TTTTTCATCTTGTATCCTTCAGGTCCTCTCGCCCCTGGCCA	ttca\|GGTC
Acc marginally increased	1583	wt: 0.3592 / mu: 0.3749 (marginal change - not scored)	wt: TGTATCCTTCAGGTCCTCTTGCCCCTGGCCAATGTGGCATT mu: TGTATCCTTCAGGTCCTCTCGCCCCTGGCCAATGTGGCATT	cttg\|CCCC
Acc marginally increased	1586	wt: 0.2446 / mu: 0.2672 (marginal change - not scored)	wt: ATCCTTCAGGTCCTCTTGCCCCTGGCCAATGTGGCATTAAT mu: ATCCTTCAGGTCCTCTCGCCCCTGGCCAATGTGGCATTAAT	gccc\|CTGG
Acc marginally increased	1588	wt: 0.8656 / mu: 0.8684 (marginal change - not scored)	wt: CCTTCAGGTCCTCTTGCCCCTGGCCAATGTGGCATTAATTG mu: CCTTCAGGTCCTCTCGCCCCTGGCCAATGTGGCATTAATTG	ccct\|GGCC

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

all identical

ENSGALG00000008376

Trubripes

no homologue

Drerio

all identical

ENSDARG00000074995

Dmelanogaster

all identical

FBgn0023512

Celegans

all conserved

D2085.3

Xtropicalis

all conserved

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

203

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

224

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

1582

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

183854407

original gDNA sequence snippet

TTGTATCCTTCAGGTCCTCTTGCCCCTGGCCAATGTGGCAT

altered gDNA sequence snippet

TTGTATCCTTCAGGTCCTCTCGCCCCTGGCCAATGTGGCAT

original cDNA sequence snippet

GGACCAGCCTCGGGTCCTCTTGCCCCTGGCCAATGTGGCAT

altered cDNA sequence snippet

GGACCAGCCTCGGGTCCTCTCGCCCCTGGCCAATGTGGCAT

wildtype AA sequence

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

mutated AA sequence

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

speed

0.16 s

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999998504522557 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM051468)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:183854407T>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.203T>C
cDNA.213T>C
g.1582T>C

AA changes

L68S Score: 145 explain score(s)

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

frameshift

known variant

Reference ID: rs113994044

database	homozygous (C/C)	heterozygous	allele carriers
1000G	-	-	-
ExAC	0	1	1

regulatory features

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.041	0.991
	4.987	1
(flanking)	0.435	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 marginally increased	1573	wt: 0.9319 / mu: 0.9350 (marginal change - not scored)	wt: TTTTTCATCTTGTATCCTTCAGGTCCTCTTGCCCCTGGCCA mu: TTTTTCATCTTGTATCCTTCAGGTCCTCTCGCCCCTGGCCA	ttca\|GGTC
Acc marginally increased	1583	wt: 0.3592 / mu: 0.3749 (marginal change - not scored)	wt: TGTATCCTTCAGGTCCTCTTGCCCCTGGCCAATGTGGCATT mu: TGTATCCTTCAGGTCCTCTCGCCCCTGGCCAATGTGGCATT	cttg\|CCCC
Acc marginally increased	1586	wt: 0.2446 / mu: 0.2672 (marginal change - not scored)	wt: ATCCTTCAGGTCCTCTTGCCCCTGGCCAATGTGGCATTAAT mu: ATCCTTCAGGTCCTCTCGCCCCTGGCCAATGTGGCATTAAT	gccc\|CTGG
Acc marginally increased	1588	wt: 0.8656 / mu: 0.8684 (marginal change - not scored)	wt: CCTTCAGGTCCTCTTGCCCCTGGCCAATGTGGCATTAATTG mu: CCTTCAGGTCCTCTCGCCCCTGGCCAATGTGGCATTAATTG	ccct\|GGCC

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

all identical

ENSGALG00000008376

Trubripes

no homologue

Drerio

all identical

ENSDARG00000074995

Dmelanogaster

all identical

FBgn0023512

Celegans

all conserved

D2085.3

Xtropicalis

all conserved

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

203

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

213

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

1582

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

183854407

original gDNA sequence snippet

TTGTATCCTTCAGGTCCTCTTGCCCCTGGCCAATGTGGCAT

altered gDNA sequence snippet

TTGTATCCTTCAGGTCCTCTCGCCCCTGGCCAATGTGGCAT

original cDNA sequence snippet

GGACCAGCCTCGGGTCCTCTTGCCCCTGGCCAATGTGGCAT

altered cDNA sequence snippet

GGACCAGCCTCGGGTCCTCTCGCCCCTGGCCAATGTGGCAT

wildtype AA sequence

mutated AA sequence

speed

0.27 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems