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 3.82059 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
EIF2B5	disease_causing_automatic	0.999994915871003	simple_aae			0	S447L	single base exchange	rs113994080		show file
EIF2B5	disease_causing_automatic	0.999994915871003	simple_aae			0	S447L	single base exchange	rs113994080		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999994915871003 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM032888)
known disease mutation: rs813359 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:183860062C>TN/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.1340C>T
cDNA.1462C>T
g.7237C>T

AA changes

S447L Score: 145 explain score(s)

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

447

frameshift

known variant

Reference ID: rs113994080
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs813359 (pathogenic for Leukoencephalopathy with vanishing white matter) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM032888)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032888)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032888)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.312	1
	6.112	1
(flanking)	-1.939	0.026

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

447

mutated

not conserved

447

Ptroglodytes

all identical

ENSPTRG00000015679

447

Mmulatta

all identical

ENSMMUG00000006562

447

Fcatus

all identical

ENSFCAG00000007787

447

Mmusculus

all identical

ENSMUSG00000003235

443

Ggallus

all conserved

ENSGALG00000008376

433

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000074995

429

Dmelanogaster

all conserved

FBgn0023512

412

Celegans

not conserved

D2085.3

416

Xtropicalis

all conserved

ENSXETG00000014293

444

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

1340

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

1462

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

7237

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

183860062

original gDNA sequence snippet

TATCACGCTGCCTGAGGGCTCGGTGATCTCTTTGCACCCTC

altered gDNA sequence snippet

TATCACGCTGCCTGAGGGCTTGGTGATCTCTTTGCACCCTC

original cDNA sequence snippet

TATCACGCTGCCTGAGGGCTCGGTGATCTCTTTGCACCCTC

altered cDNA sequence snippet

TATCACGCTGCCTGAGGGCTTGGTGATCTCTTTGCACCCTC

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
SNLHMYSAVC ADVIRRWVYP LTPEANFTDS TTQSCTHSRH NIYRGPEVSL GHGSILEENV
LLGSGTVIGS NCFITNSVIG PGCHIGDNVV LDQTYLWQGV RVAAGAQIHQ SLLCDNAEVK
ERVTLKPRSV LTSQVVVGPN ITLPEGLVIS 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

1.01 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: 0.999994915871003 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM032888)
known disease mutation: rs813359 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:183860062C>TN/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.1340C>T
cDNA.1350C>T
g.7237C>T

AA changes

S447L Score: 145 explain score(s)

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

447

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.312	1
	6.112	1
(flanking)	-1.939	0.026

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

447

mutated

not conserved

447

Ptroglodytes

all identical

ENSPTRG00000015679

447

Mmulatta

all identical

ENSMMUG00000006562

447

Fcatus

all identical

ENSFCAG00000007787

447

Mmusculus

all identical

ENSMUSG00000003235

443

Ggallus

all conserved

ENSGALG00000008376

433

Trubripes

no homologue

Drerio

all conserved

ENSDARG00000074995

429

Dmelanogaster

all conserved

FBgn0023512

412

Celegans

not conserved

D2085.3

416

Xtropicalis

all conserved

ENSXETG00000014293

444

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

1340

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

1350

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

7237

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

183860062

original gDNA sequence snippet

TATCACGCTGCCTGAGGGCTCGGTGATCTCTTTGCACCCTC

altered gDNA sequence snippet

TATCACGCTGCCTGAGGGCTTGGTGATCTCTTTGCACCCTC

original cDNA sequence snippet

TATCACGCTGCCTGAGGGCTCGGTGATCTCTTTGCACCCTC

altered cDNA sequence snippet

TATCACGCTGCCTGAGGGCTTGGTGATCTCTTTGCACCCTC

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
SNLHMYSAVC ADVIRRWVYP LTPEANFTDS TTQSCTHSRH NIYRGPEVSL GHGSILEENV
LLGSGTVIGS NCFITNSVIG PGCHIGDNVV LDQTYLWQGV RVAAGAQIHQ SLLCDNAEVK
ERVTLKPRSV LTSQVVVGPN ITLPEGLVIS 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

0.86 s

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

mutation t@sting

Prediction

disease causing

Problems