Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
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 2.839704 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
EPM2Adisease_causing0.999999997971325simple_aaeaffectedR171Hsingle base exchangers137852916show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999997971325      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM994483)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr6:145956587C>TN/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.512G>A
cDNA.1038G>A
g.100574G>A
AA changes R171H Score: 29 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 171
frameshift no
known variant Reference ID: rs137852916
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC044

known disease mutation at this position, please check HGMD for details (HGMD ID CM994483)

known disease mutation at this position, please check HGMD for details (HGMD ID CM994483)
known disease mutation at this position, please check HGMD for details (HGMD ID CM994483)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.6280.7
5.8711
(flanking)5.8711
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased100577wt: 0.8017 / mu: 0.8390 (marginal change - not scored)wt: GCTGGGTAGCTGCCCTCGTCAGGTGGAACATGTAACCATCA
mu: GCTGGGTAGCTGCCCTCATCAGGTGGAACATGTAACCATCA		 gtca|GGTG
Donor increased100578wt: 0.63 / mu: 0.89wt: CGTCAGGTGGAACAT
mu: CATCAGGTGGAACAT		 TCAG|gtgg
distance from splice site 36
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      171ILPNIWLGSCPRQVEHVTIKLKHE
mutated  not conserved    171ILPNIWLGSCPHQVEHVTIKL
Ptroglodytes  all identical  ENSPTRG00000018681  171ILPNIWLGSCPRQVEHVTIKL
Mmulatta  all identical  ENSMMUG00000010643  171ILPNIWLGSCPRQVEHVTIKL
Fcatus  all identical  ENSFCAG00000011712  70PNIWLGSCPRQVEHVTIKLKH
Mmusculus  all identical  ENSMUSG00000055493  170ILPNIWLGSCPRQLEHVTIKL
Ggallus  all identical  ENSGALG00000012275  158ILPNIWLGSCPRQLEHVTVKL
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000059044  154VLPRVWLGSCPRRVEHVTLKLKQ
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000017691  153ILPNIWLGSCPRQREHVTVKM
protein features
start (aa)end (aa)featuredetails 
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 512
cDNA position
(for ins/del: last normal base / first normal base)		 1038
gDNA position
(for ins/del: last normal base / first normal base)		 100574
chromosomal position
(for ins/del: last normal base / first normal base)		 145956587
original gDNA sequence snippet CTGGCTGGGTAGCTGCCCTCGTCAGGTGGAACATGTAACCA
altered gDNA sequence snippet CTGGCTGGGTAGCTGCCCTCATCAGGTGGAACATGTAACCA
original cDNA sequence snippet CTGGCTGGGTAGCTGCCCTCGTCAGGTGGAACATGTAACCA
altered cDNA sequence snippet CTGGCTGGGTAGCTGCCCTCATCAGGTGGAACATGTAACCA
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 RWEPRGAVRL RPAGTAAGDG ALALQEPGLW
LGEVELAAEE AAQDGAEPGR VDTFWYKFLK REPGGELSWE GNGPHHDRCC TYNENNLVDG
VYCLPIGHWI EATGHTNEMK HTTDFYFNIA GHQAMHYSRI LPNIWLGSCP HQVEHVTIKL
KHELGITAVM NFQTEWDIVQ NSSGCNRYPE PMTPDTMIKL YREEGLAYIW MPTPDMSTEG
RVQMLPQAVC LLHALLEKGH IVYVHCNAGV GRSTAAVCGW LQYVMGWNLR KVQYFLMAKR
PAVYIDEEAL ARAQEDFFQK FGKVRSSVCS L*
speed 0.82 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