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 3.692222 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
EIF2B5	disease_causing	0.999999999915326	simple_aae		affected		E650K	single base exchange	rs113994085		show file
EIF2B5	disease_causing	0.999999999915326	simple_aae		affected		E650K	single base exchange	rs113994085		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999915326 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM013544)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:183861965G>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.1948G>A
cDNA.2070G>A
g.9140G>A

AA changes

E650K Score: 56 explain score(s)

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

650

frameshift

known variant

Reference ID: rs113994085
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation at this position, please check HGMD for details (HGMD ID CM013544)

known disease mutation at this position, please check HGMD for details (HGMD ID CM013544)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013544)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.333	0.939
	5.814	1
(flanking)	4.806	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
Donor increased	9136	wt: 0.45 / mu: 0.75	wt: GCAGCCATTGAGGAC mu: GCAGCCATTAAGGAC	AGCC\|attg
Donor marginally increased	9137	wt: 0.5414 / mu: 0.5763 (marginal change - not scored)	wt: CAGCCATTGAGGACT mu: CAGCCATTAAGGACT	GCCA\|ttga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

650

mutated

all conserved

650

Ptroglodytes

all identical

ENSPTRG00000015679

650

Mmulatta

all identical

ENSMMUG00000006562

650

Fcatus

all identical

ENSFCAG00000007787

650

Mmusculus

all identical

ENSMUSG00000003235

646

Ggallus

all identical

ENSGALG00000008376

634

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000074995

n/a

Dmelanogaster

all identical

FBgn0023512

598

Celegans

all identical

D2085.3

578

LKVKSADQKRFELDLKRRCQI

Xtropicalis

all identical

ENSXETG00000014293

646

protein features

start (aa)	end (aa)	feature	details
543	720	DOMAIN	W2.	lost
639	655	HELIX		lost
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

1948

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

2070

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

9140

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

183861965

original gDNA sequence snippet

TGGAAGCGTTAGCAGCCATTGAGGACTTCTTCCTAGAGCAT

altered gDNA sequence snippet

TGGAAGCGTTAGCAGCCATTAAGGACTTCTTCCTAGAGCAT

original cDNA sequence snippet

TGGAAGCGTTAGCAGCCATTGAGGACTTCTTCCTAGAGCAT

altered cDNA sequence snippet

TGGAAGCGTTAGCAGCCATTAAGGACTTCTTCCTAGAGCAT

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 ITLPEGSVIS LHPPDAEEDE DDGEFSDDSG ADQEKDKVKM
KGYNPAEVGA AGKGYLWKAA GMNMEEEEEL QQNLWGLKIN MEEESESESE QSMDSEEPDS
RGGSPQMDDI KVFQNEVLGT LQRGKEENIS CDNLVLEINS LKYAYNISLK EVMQVLSHVV
LEFPLQQMDS PLDSSRYCAL LLPLLKAWSP VFRNYIKRAA DHLEALAAIK DFFLEHEALG
ISMAKVLMAF YQLEILAEET ILSWFSQRDT TDKGQQLRKN QQLQRFIQWL KEAEEESSED
D*

speed

0.86 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: 0.999999999915326 (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM013544)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr3:183861965G>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.1948G>A
cDNA.1958G>A
g.9140G>A

AA changes

E650K Score: 56 explain score(s)

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

650

frameshift

known variant

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	-0.333	0.939
	5.814	1
(flanking)	4.806	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
Donor increased	9136	wt: 0.45 / mu: 0.75	wt: GCAGCCATTGAGGAC mu: GCAGCCATTAAGGAC	AGCC\|attg
Donor marginally increased	9137	wt: 0.5414 / mu: 0.5763 (marginal change - not scored)	wt: CAGCCATTGAGGACT mu: CAGCCATTAAGGACT	GCCA\|ttga

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

650

mutated

all conserved

650

Ptroglodytes

all identical

ENSPTRG00000015679

650

Mmulatta

all identical

ENSMMUG00000006562

650

Fcatus

all identical

ENSFCAG00000007787

650

Mmusculus

all identical

ENSMUSG00000003235

646

Ggallus

all identical

ENSGALG00000008376

634

Trubripes

no homologue

Drerio

no alignment

ENSDARG00000074995

n/a

Dmelanogaster

all identical

FBgn0023512

598

Celegans

all identical

D2085.3

578

LKVKSADQKRFELDLKRRCQI

Xtropicalis

all identical

ENSXETG00000014293

646

protein features

start (aa)	end (aa)	feature	details
543	720	DOMAIN	W2.	lost
639	655	HELIX		lost
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

1948

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

1958

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

9140

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

183861965

original gDNA sequence snippet

TGGAAGCGTTAGCAGCCATTGAGGACTTCTTCCTAGAGCAT

altered gDNA sequence snippet

TGGAAGCGTTAGCAGCCATTAAGGACTTCTTCCTAGAGCAT

original cDNA sequence snippet

TGGAAGCGTTAGCAGCCATTGAGGACTTCTTCCTAGAGCAT

altered cDNA sequence snippet

TGGAAGCGTTAGCAGCCATTAAGGACTTCTTCCTAGAGCAT

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 ITLPEGSVIS LHPPDAEEDE DDGEFSDDSG ADQEKDKVKM
KGYNPAEVGA AGKGYLWKAA GMNMEEEEEL QQNLWGLKIN MEEESESESE QSMDSEEPDS
RGGSPQMDDI KVFQNEVLGT LQRGKEENIS CDNLVLEINS LKYAYNISLK EVMQVLSHVV
LEFPLQQMDS PLDSSRYCAL LLPLLKAWSP VFRNYIKRAA DHLEALAAIK 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