Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM013533)
  • known disease mutation: rs195203 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr3:183854522A>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.318A>T
cDNA.328A>T
g.1697A>T
AA changes L106F Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 106
frameshift no
known variant Reference ID: rs113994048
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC066

known disease mutation: rs195203 (pathogenic for Leukoencephalopathy with vanishing white matter|Inborn genetic diseases|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM013533)

known disease mutation at this position, please check HGMD for details (HGMD ID CM013533)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013533)
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
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)5.110.983
-0.7530.294
(flanking)1.3380.562
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
Donor lost1698sequence motif lost- wt: TACT|gtaa
 mu: TTCT.gtaa
Donor decreased1698wt: 0.86 / mu: 0.41wt: ATTTACTGTAAGGCC
mu: ATTTTCTGTAAGGCC		 TTAC|tgta
Acc gained17030.66mu: ATCAAAGAACATTTTCTGTAAGGCCCTGCAACTTTTCTTTC gtaa|GGCC
distance from splice site 3
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      106CCWKAAQIKEHLLKSKWCRPTSLN
mutated  not conserved    106CCWKAAQIKEHFLKSKWCRPTSL
Ptroglodytes  all identical  ENSPTRG00000015679  106CCWKAAQIKEHLLKSKWCRPTSL
Mmulatta  all identical  ENSMMUG00000006562  106CCWKAAQIKEHLLKSKWCRPTSL
Fcatus  all identical  ENSFCAG00000007787  106CCWKAAQIKEHLLKSKWCRPTSL
Mmusculus  all identical  ENSMUSG00000003235  102CCWKAAQIKEHLQKSKWCHPTSP
Ggallus  all identical  ENSGALG00000008376  92CCWKSAEIKEHLQKSKWCRHTSP
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000074995  88CWMSSKIKEHLLKSKWCRPTSP
Dmelanogaster  not conserved  FBgn0023512  72REHIRAGIATDAAWSFKMT-
Celegans  not conserved  D2085.3  83---DHATSVQREWRLAF
Xtropicalis  all identical  ENSXETG00000014293  102CCWMANDIKEHLRNSKWCRPTSP
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 318
cDNA position
(for ins/del: last normal base / first normal base)		 328
gDNA position
(for ins/del: last normal base / first normal base)		 1697
chromosomal position
(for ins/del: last normal base / first normal base)		 183854522
original gDNA sequence snippet GCTCAAATCAAAGAACATTTACTGTAAGGCCCTGCAACTTT
altered gDNA sequence snippet GCTCAAATCAAAGAACATTTTCTGTAAGGCCCTGCAACTTT
original cDNA sequence snippet GCTCAAATCAAAGAACATTTACTGAAGTCAAAGTGGTGCCG
altered cDNA sequence snippet GCTCAAATCAAAGAACATTTTCTGAAGTCAAAGTGGTGCCG
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 QIKEHFLKSK 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*
speed 0.55 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