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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 1 transcript(s)...
Querying Taster for transcript #1: ENST00000367519
MT speed 0 s - this script 2.508831 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
EPM2Adisease_causing0.999926273656659simple_aaeaffectedW32Gsingle base exchangers104893955show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.999926273656659      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs3107 (probable pathogenic)
  • known disease mutation at this position (HGMD CM004467)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:146056541A>CN/A show variant in all transcripts   IGV
HGNC symbol EPM2A
Ensembl transcript ID ENST00000367519
Genbank transcript ID NM_005670
UniProt peptide O95278
alteration type single base exchange
alteration region CDS
DNA changes c.94T>G
cDNA.620T>G
g.620T>G
AA changes W32G Score: 184 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 32
frameshift no
known variant Reference ID: rs104893955
Allele 'C' was neither found in ExAC nor 1000G.
known as potential disease variant: rs3107 (probable pathogenic for Lafora disease|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM004467)

known disease mutation at this position, please check HGMD for details (HGMD ID CM004467)
known disease mutation at this position, please check HGMD for details (HGMD ID CM004467)
regulatory features ELF1, Transcription Factor, ELF1 Transcription Factor Binding
Promoter Associated, Regulatory Feature, Promoter like regulatory feature
Max, Transcription Factor, Max TF binding
E2F6, Transcription Factor, E2F6 Transcription Factor Binding
PolII, Polymerase, RNA Polymerase II
H4K91ac, Histone, Histone 4 Lysine 91 Acetylation
E2F4, Transcription Factor, E2F4 Transcription Factor Binding
HEY1, Transcription Factor, HEY1 Transcription Factor Binding
Cmyc, Transcription Factor, Cmyc TF binding
H3K9ac, Histone, Histone 3 Lysine 9 Acetylation
Yy1, Transcription Factor, Yy1 Transcription Factor Binding
Sin3Ak20, Transcription Factor, Sin3Ak20 Transcription Factor Binding
H3K27ac, Histone, Histone 3 Lysine 27 Acetylation
TAF1, Transcription Factor, TAF1 Transcription Factor Binding
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
EBF, Transcription Factor, EBF Transcription Factor Binding
E2F1, Transcription Factor, E2F1 Transcription Factor Binding
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)2.721
1.0550.994
(flanking)0.5830.97
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased612wt: 0.41 / mu: 0.53wt: CGAGCTGGGGCGTTG
mu: CGAGCTGGGGCGTGG		 AGCT|gggg
Donor gained6190.62mu: GGGCGTGGGGAGCCG GCGT|gggg
distance from splice site 208
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      32LVVGSRPELGRWEPRGAVRLRPAG
mutated  not conserved    32LVVGSRPELGRGEPRGAVRLRPA
Ptroglodytes  all identical  ENSPTRG00000018681  32LVVGSRPELGRWEPRGAVRLRPA
Mmulatta  all identical  ENSMMUG00000010643  32LVVGSRPELGRWEPRGAVRLRPA
Fcatus  no alignment  ENSFCAG00000011712  n/a
Mmusculus  all identical  ENSMUSG00000055493  32LLAGSRPELGRWEPHGAVRLRPA
Ggallus  all identical  ENSGALG00000012275  32LVAGSRPELGEWDPQRAVPMQPA
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000059044  34FVLGSRPEMGLWDTERAVKMNPS
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000017691  32LVLGSRKEMGSWDPQYAVPMKPT
protein features
start (aa)end (aa)featuredetails 
1124DOMAINCBM20.lost
8787MUTAGENK->A: Partial loss of phosphatase activity. Abolishes glycogen binding.might get lost (downstream of altered splice site)
168168MUTAGENS->A,D: Abolishes interaction with NHLRC1.might get lost (downstream of altered splice site)
187187MUTAGENT->D: Abolishes interaction with NHLRC1.might get lost (downstream of altered splice site)
193193CONFLICTQ -> K (in Ref. 8; AAH70047).might get lost (downstream of altered splice site)
194194MUTAGENT->D: Does not affect interaction with NHLRC1, PPP1R3C or PRKAA2.might get lost (downstream of altered splice site)
235235MUTAGEND->A: Loss of phosphatase activity. Does not affect glycogen binding.might get lost (downstream of altered splice site)
243311DOMAINTyrosine-protein phosphatase.might get lost (downstream of altered splice site)
248248CONFLICTA -> P (in Ref. 4; AAO15523).might get lost (downstream of altered splice site)
258258CONFLICTK -> E (in Ref. 5; BAG61454).might get lost (downstream of altered splice site)
266266MUTAGENC->S: Complete loss of phosphatase activity. Does not affect glycogen binding. Does not affect self- interaction. Increases the interaction with PPP1R3C.might get lost (downstream of altered splice site)
294294CONFLICTY -> H (in Ref. 5; BAG61454).might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 996 / 996
position (AA) of stopcodon in wt / mu AA sequence 332 / 332
position of stopcodon in wt / mu cDNA 1522 / 1522
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 527 / 527
chromosome 6
strand -1
last intron/exon boundary 1245
theoretical NMD boundary in CDS 668
length of CDS 996
coding sequence (CDS) position 94
cDNA position
(for ins/del: last normal base / first normal base)		 620
gDNA position
(for ins/del: last normal base / first normal base)		 620
chromosomal position
(for ins/del: last normal base / first normal base)		 146056541
original gDNA sequence snippet CGCGGCCCGAGCTGGGGCGTTGGGAGCCGCGCGGTGCCGTC
altered gDNA sequence snippet CGCGGCCCGAGCTGGGGCGTGGGGAGCCGCGCGGTGCCGTC
original cDNA sequence snippet CGCGGCCCGAGCTGGGGCGTTGGGAGCCGCGCGGTGCCGTC
altered cDNA sequence snippet CGCGGCCCGAGCTGGGGCGTGGGGAGCCGCGCGGTGCCGTC
wildtype AA sequence MRFRFGVVVP PAVAGARPEL LVVGSRPELG RWEPRGAVRL RPAGTAAGDG ALALQEPGLW
LGEVELAAEE AAQDGAEPGR VDTFWYKFLK REPGGELSWE GNGPHHDRCC TYNENNLVDG
VYCLPIGHWI EATGHTNEMK HTTDFYFNIA GHQAMHYSRI LPNIWLGSCP RQVEHVTIKL
KHELGITAVM NFQTEWDIVQ NSSGCNRYPE PMTPDTMIKL YREEGLAYIW MPTPDMSTEG
RVQMLPQAVC LLHALLEKGH IVYVHCNAGV GRSTAAVCGW LQYVMGWNLR KVQYFLMAKR
PAVYIDEEAL ARAQEDFFQK FGKVRSSVCS L*
mutated AA sequence MRFRFGVVVP PAVAGARPEL LVVGSRPELG RGEPRGAVRL RPAGTAAGDG ALALQEPGLW
LGEVELAAEE AAQDGAEPGR VDTFWYKFLK REPGGELSWE GNGPHHDRCC TYNENNLVDG
VYCLPIGHWI EATGHTNEMK HTTDFYFNIA GHQAMHYSRI LPNIWLGSCP RQVEHVTIKL
KHELGITAVM NFQTEWDIVQ NSSGCNRYPE PMTPDTMIKL YREEGLAYIW MPTPDMSTEG
RVQMLPQAVC LLHALLEKGH IVYVHCNAGV GRSTAAVCGW LQYVMGWNLR KVQYFLMAKR
PAVYIDEEAL ARAQEDFFQK FGKVRSSVCS L*
speed 0.45 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
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