Yum, tasty mutations...

MutationTaster - study a chromosomal position

MTQE documentation
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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 2.97 s - this script 5.961323 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
EIF2B5disease_causing0.999999975847798simple_aaeY495Csingle base exchangers113994082show file
EIF2B5disease_causing0.999999975847798simple_aaeY495Csingle base exchangers113994082show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999975847798      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM032889)
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:183860329A>GN/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.1484A>G
cDNA.1606A>G
g.7504A>G
AA changes Y495C Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS
495
frameshift no
known variant Reference ID: rs113994082
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC011

known disease mutation at this position, please check HGMD for details (HGMD ID CM032889)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032889)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032889)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.5531
5.1221
(flanking)1.9571
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased7509wt: 0.9894 / mu: 0.9912 (marginal change - not scored)wt: ACCTCTGGAAAGCTG
mu: GCCTCTGGAAAGCTG
 CTCT|ggaa
distance from splice site 40
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      495NPAEVGAAGKGYLWKAAGMNMEEE
mutated  not conserved    495NPAEVGAAGKGCLWKAAGMNMEE
Ptroglodytes  all identical  ENSPTRG00000015679  495NPAEVGAAGKGYLWKAAGMNMEE
Mmulatta  all identical  ENSMMUG00000006562  495NPAEVGVAGKGYLWKAAGMNMEE
Fcatus  all identical  ENSFCAG00000007787  495NPAEVGVAGQGYLWKAADMNVEE
Mmusculus  all identical  ENSMUSG00000003235  491NPAEVGLEGQGYLWKAEGVNSKE
Ggallus  all identical  ENSGALG00000008376  481NKKDVGSEGRGYLWK
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000074995  477NPAEVGSEGKGYRWKSSSLDDTE
Dmelanogaster  not conserved  FBgn0023512  459HAYIVSDLTTGDPEDSECEDLLP
Celegans  not conserved  D2085.3  449GNVHVSKFRNGGPFWRRSVNGKT
Xtropicalis  all identical  ENSXETG00000014293  491EGQGYLWKFSNLAEEE
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 3
strand 1
last intron/exon boundary 2229
theoretical NMD boundary in CDS 2056
length of CDS 2166
coding sequence (CDS) position 1484
cDNA position
(for ins/del: last normal base / first normal base)
1606
gDNA position
(for ins/del: last normal base / first normal base)
7504
chromosomal position
(for ins/del: last normal base / first normal base)
183860329
original gDNA sequence snippet AGGAGCTGCTGGCAAGGGCTACCTCTGGAAAGCTGCAGGCA
altered gDNA sequence snippet AGGAGCTGCTGGCAAGGGCTGCCTCTGGAAAGCTGCAGGCA
original cDNA sequence snippet AGGAGCTGCTGGCAAGGGCTACCTCTGGAAAGCTGCAGGCA
altered cDNA sequence snippet AGGAGCTGCTGGCAAGGGCTGCCTCTGGAAAGCTGCAGGCA
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 AGKGCLWKAA GMNMEEEEEL QQNLWGLKIN MEEESESESE QSMDSEEPDS
RGGSPQMDDI KVFQNEVLGT LQRGKEENIS CDNLVLEINS LKYAYNISLK EVMQVLSHVV
LEFPLQQMDS PLDSSRYCAL LLPLLKAWSP VFRNYIKRAA DHLEALAAIE DFFLEHEALG
ISMAKVLMAF YQLEILAEET ILSWFSQRDT TDKGQQLRKN QQLQRFIQWL KEAEEESSED
D*
speed 1.57 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
Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999975847798      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM032889)
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:183860329A>GN/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.1484A>G
cDNA.1494A>G
g.7504A>G
AA changes Y495C Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS
495
frameshift no
known variant Reference ID: rs113994082
databasehomozygous (G/G)heterozygousallele carriers
1000G---
ExAC011

known disease mutation at this position, please check HGMD for details (HGMD ID CM032889)

known disease mutation at this position, please check HGMD for details (HGMD ID CM032889)
known disease mutation at this position, please check HGMD for details (HGMD ID CM032889)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.5531
5.1221
(flanking)1.9571
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased7509wt: 0.9894 / mu: 0.9912 (marginal change - not scored)wt: ACCTCTGGAAAGCTG
mu: GCCTCTGGAAAGCTG
 CTCT|ggaa
distance from splice site 40
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      495NPAEVGAAGKGYLWKAAGMNMEEE
mutated  not conserved    495NPAEVGAAGKGCLWKAAGMNMEE
Ptroglodytes  all identical  ENSPTRG00000015679  495NPAEVGAAGKGYLWKAAGMNMEE
Mmulatta  all identical  ENSMMUG00000006562  495NPAEVGVAGKGYLWKAAGMNMEE
Fcatus  all identical  ENSFCAG00000007787  495NPAEVGVAGQGYLWKAADMNVEE
Mmusculus  all identical  ENSMUSG00000003235  491NPAEVGLEGQGYLWKAEGVNSKE
Ggallus  all identical  ENSGALG00000008376  481NKKDVGSEGRGYLWK
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000074995  477NPAEVGSEGKGYRWKSSSLDDTE
Dmelanogaster  not conserved  FBgn0023512  459HAYIVSDLTTGDPEDSECEDLLP
Celegans  not conserved  D2085.3  449GNVHVSKFRNGGPFWRRSVNGKT
Xtropicalis  all identical  ENSXETG00000014293  491EGQGYLWKFSNLAEEE
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 3
strand 1
last intron/exon boundary 2117
theoretical NMD boundary in CDS 2056
length of CDS 2118
coding sequence (CDS) position 1484
cDNA position
(for ins/del: last normal base / first normal base)
1494
gDNA position
(for ins/del: last normal base / first normal base)
7504
chromosomal position
(for ins/del: last normal base / first normal base)
183860329
original gDNA sequence snippet AGGAGCTGCTGGCAAGGGCTACCTCTGGAAAGCTGCAGGCA
altered gDNA sequence snippet AGGAGCTGCTGGCAAGGGCTGCCTCTGGAAAGCTGCAGGCA
original cDNA sequence snippet AGGAGCTGCTGGCAAGGGCTACCTCTGGAAAGCTGCAGGCA
altered cDNA sequence snippet AGGAGCTGCTGGCAAGGGCTGCCTCTGGAAAGCTGCAGGCA
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 QQVVC*
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 AGKGCLWKAA GMNMEEEEEL QQNLWGLKIN MEEESESESE QSMDSEEPDS
RGGSPQMDDI KVFQNEVLGT LQRGKEENIS CDNLVLEINS LKYAYNISLK EVMQVLSHVV
LEFPLQQMDS PLDSSRYCAL LLPLLKAWSP VFRNYIKRAA DHLEALAAIE DFFLEHEALG
ISMAKVLMAF YQLEILAEET ILSWFSQRDT TDKGQQLRKN QQVVC*
speed 1.40 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

Problems