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 2.27 s - this script 5.000117 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
EIF2B5disease_causing_automatic0.999999999999999simple_aaeaffected0G386Vsingle base exchangers113994074show file
EIF2B5disease_causing_automatic0.999999999999999simple_aaeaffected0G386Vsingle base exchangers113994074show file

Taster files

Yum, tasty mutations...

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999999999 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM013541)
  • known disease mutation: rs5944 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:183859713G>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.1157G>T
cDNA.1279G>T
g.6888G>T
AA changes G386V Score: 109 explain score(s)
position(s) of altered AA
if AA alteration in CDS
386
frameshift no
known variant Reference ID: rs113994074
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs5944 (pathogenic for Leukoencephalopathy with vanishing white matter) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM013541)

known disease mutation at this position, please check HGMD for details (HGMD ID CM013541)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013541)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.7551
5.7551
(flanking)0.8981
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost6887sequence motif lost- wt: ccag|GTGA
 mu: ccag.TTGA
Acc increased6879wt: 0.48 / mu: 0.55wt: TACCCAGAGGTCTTCCCATCCTGAGCCAGGTGATAACGTGG
mu: TACCCAGAGGTCTTCCCATCCTGAGCCAGTTGATAACGTGG
 atcc|TGAG
Acc lost68870.35wt: GGTCTTCCCATCCTGAGCCAGGTGATAACGTGGTGCTGGAC ccag|GTGA
Donor marginally increased6889wt: 0.2085 / mu: 0.2106 (marginal change - not scored)wt: CCAGGTGATAACGTG
mu: CCAGTTGATAACGTG
 AGGT|gata
Donor marginally increased6890wt: 0.8541 / mu: 0.9304 (marginal change - not scored)wt: CAGGTGATAACGTGG
mu: CAGTTGATAACGTGG
 GGTG|ataa
Donor increased6886wt: 0.54 / mu: 0.75wt: GAGCCAGGTGATAAC
mu: GAGCCAGTTGATAAC
 GCCA|ggtg
Acc gained68860.37mu: AGGTCTTCCCATCCTGAGCCAGTTGATAACGTGGTGCTGGA gcca|GTTG
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      386TNSVIGPGCHIGDNVVLDQTYLWQ
mutated  not conserved    386TNSVIGPGCHIVDNVVLDQTYLW
Ptroglodytes  all identical  ENSPTRG00000015679  386TNSVIGPGCHIGDNVVLDQTYLW
Mmulatta  all identical  ENSMMUG00000006562  386TNSVIGPGCRIGDNVVLDQTYLW
Fcatus  all identical  ENSFCAG00000007787  386TNSVIGPGCRIGDNVVLDQAYLW
Mmusculus  all identical  ENSMUSG00000003235  382TNSVIGPNCHIGDNVVLDQAYLW
Ggallus  all identical  ENSGALG00000008376  372IGQNCRIGDEVTLDGAFLW
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000074995  368SNTVIGANCVIGDNVTLERAY
Dmelanogaster  all identical  FBgn0023512  353SDSVIGANCRIGKNCRLTN
Celegans  not conserved  D2085.3  348RNSCIGAHTEISSKTRI
Xtropicalis  all identical  ENSXETG00000014293  382SNSTIGRNCSIEGDRVVLENVHVW
protein features
start (aa)end (aa)featuredetails 
505509COMPBIASPoly-Glu.might get lost (downstream of altered splice site)
525525MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
527527MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
529529MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
532532MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
535535MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
540540MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
543720DOMAINW2.might get lost (downstream of altered splice site)
544544MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
547567HELIXmight get lost (downstream of altered splice site)
571584HELIXmight get lost (downstream of altered splice site)
589602HELIXmight get lost (downstream of altered splice site)
603607HELIXmight get lost (downstream of altered splice site)
614635HELIXmight get lost (downstream of altered splice site)
639655HELIXmight get lost (downstream of altered splice site)
657662HELIXmight get lost (downstream of altered splice site)
663672HELIXmight get lost (downstream of altered splice site)
678685HELIXmight get lost (downstream of altered splice site)
693697HELIXmight get lost (downstream of altered splice site)
701714HELIXmight get lost (downstream of altered splice site)
717717MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
718718MOD_RESPhosphoserine.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 3
strand 1
last intron/exon boundary 2229
theoretical NMD boundary in CDS 2056
length of CDS 2166
coding sequence (CDS) position 1157
cDNA position
(for ins/del: last normal base / first normal base)
1279
gDNA position
(for ins/del: last normal base / first normal base)
6888
chromosomal position
(for ins/del: last normal base / first normal base)
183859713
original gDNA sequence snippet GTCTTCCCATCCTGAGCCAGGTGATAACGTGGTGCTGGACC
altered gDNA sequence snippet GTCTTCCCATCCTGAGCCAGTTGATAACGTGGTGCTGGACC
original cDNA sequence snippet TGGCCCCGGCTGCCACATTGGTGATAACGTGGTGCTGGACC
altered cDNA sequence snippet TGGCCCCGGCTGCCACATTGTTGATAACGTGGTGCTGGACC
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 PGCHIVDNVV 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 1.13 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: 0.999999999999999 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM013541)
  • known disease mutation: rs5944 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:183859713G>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.1157G>T
cDNA.1167G>T
g.6888G>T
AA changes G386V Score: 109 explain score(s)
position(s) of altered AA
if AA alteration in CDS
386
frameshift no
known variant Reference ID: rs113994074
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs5944 (pathogenic for Leukoencephalopathy with vanishing white matter) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM013541)

known disease mutation at this position, please check HGMD for details (HGMD ID CM013541)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013541)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.7551
5.7551
(flanking)0.8981
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Acceptor lost6887sequence motif lost- wt: ccag|GTGA
 mu: ccag.TTGA
Acc increased6879wt: 0.48 / mu: 0.55wt: TACCCAGAGGTCTTCCCATCCTGAGCCAGGTGATAACGTGG
mu: TACCCAGAGGTCTTCCCATCCTGAGCCAGTTGATAACGTGG
 atcc|TGAG
Acc lost68870.35wt: GGTCTTCCCATCCTGAGCCAGGTGATAACGTGGTGCTGGAC ccag|GTGA
Donor marginally increased6889wt: 0.2085 / mu: 0.2106 (marginal change - not scored)wt: CCAGGTGATAACGTG
mu: CCAGTTGATAACGTG
 AGGT|gata
Donor marginally increased6890wt: 0.8541 / mu: 0.9304 (marginal change - not scored)wt: CAGGTGATAACGTGG
mu: CAGTTGATAACGTGG
 GGTG|ataa
Donor increased6886wt: 0.54 / mu: 0.75wt: GAGCCAGGTGATAAC
mu: GAGCCAGTTGATAAC
 GCCA|ggtg
Acc gained68860.37mu: AGGTCTTCCCATCCTGAGCCAGTTGATAACGTGGTGCTGGA gcca|GTTG
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      386TNSVIGPGCHIGDNVVLDQTYLWQ
mutated  not conserved    386TNSVIGPGCHIVDNVVLDQTYLW
Ptroglodytes  all identical  ENSPTRG00000015679  386TNSVIGPGCHIGDNVVLDQTYLW
Mmulatta  all identical  ENSMMUG00000006562  386TNSVIGPGCRIGDNVVLDQTYLW
Fcatus  all identical  ENSFCAG00000007787  386TNSVIGPGCRIGDNVVLDQAYLW
Mmusculus  all identical  ENSMUSG00000003235  382TNSVIGPNCHIGDNVVLDQAYLW
Ggallus  all identical  ENSGALG00000008376  372IGQNCRIGDEVTLDGAFLW
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000074995  368SNTVIGANCVIGDNVTLERAY
Dmelanogaster  all identical  FBgn0023512  353SDSVIGANCRIGKNCRLTN
Celegans  not conserved  D2085.3  348RNSCIGAHTEISSKTRI
Xtropicalis  all identical  ENSXETG00000014293  382SNSTIGRNCSIEGDRVVLENVHVW
protein features
start (aa)end (aa)featuredetails 
505509COMPBIASPoly-Glu.might get lost (downstream of altered splice site)
525525MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
527527MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
529529MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
532532MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
535535MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
540540MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
543720DOMAINW2.might get lost (downstream of altered splice site)
544544MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
547567HELIXmight get lost (downstream of altered splice site)
571584HELIXmight get lost (downstream of altered splice site)
589602HELIXmight get lost (downstream of altered splice site)
603607HELIXmight get lost (downstream of altered splice site)
614635HELIXmight get lost (downstream of altered splice site)
639655HELIXmight get lost (downstream of altered splice site)
657662HELIXmight get lost (downstream of altered splice site)
663672HELIXmight get lost (downstream of altered splice site)
678685HELIXmight get lost (downstream of altered splice site)
693697HELIXmight get lost (downstream of altered splice site)
701714HELIXmight get lost (downstream of altered splice site)
717717MOD_RESPhosphoserine.might get lost (downstream of altered splice site)
718718MOD_RESPhosphoserine.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 3
strand 1
last intron/exon boundary 2117
theoretical NMD boundary in CDS 2056
length of CDS 2118
coding sequence (CDS) position 1157
cDNA position
(for ins/del: last normal base / first normal base)
1167
gDNA position
(for ins/del: last normal base / first normal base)
6888
chromosomal position
(for ins/del: last normal base / first normal base)
183859713
original gDNA sequence snippet GTCTTCCCATCCTGAGCCAGGTGATAACGTGGTGCTGGACC
altered gDNA sequence snippet GTCTTCCCATCCTGAGCCAGTTGATAACGTGGTGCTGGACC
original cDNA sequence snippet TGGCCCCGGCTGCCACATTGGTGATAACGTGGTGCTGGACC
altered cDNA sequence snippet TGGCCCCGGCTGCCACATTGTTGATAACGTGGTGCTGGACC
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 PGCHIVDNVV 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*
speed 1.14 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

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