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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: ENST00000373960
MT speed 0 s - this script 3.395353 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
DESdisease_causing_automatic0.999506035278341simple_aaeaffected0Q389Psingle base exchangers121913004show file

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Prediction

disease causing

Model: simple_aae, prob: 0.999506035278341 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM013258)
  • known disease mutation: rs16830 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:220286204A>CN/A show variant in all transcripts   IGV
HGNC symbol DES
Ensembl transcript ID ENST00000373960
Genbank transcript ID NM_001927
UniProt peptide P17661
alteration type single base exchange
alteration region CDS
DNA changes c.1166A>C
cDNA.1252A>C
g.3106A>C
AA changes Q389P Score: 76 explain score(s)
position(s) of altered AA
if AA alteration in CDS
389
frameshift no
known variant Reference ID: rs121913004
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs16830 (pathogenic for Myofibrillar myopathy 1|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM013258)

known disease mutation at this position, please check HGMD for details (HGMD ID CM013258)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013258)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)4.2131
3.3071
(flanking)1.7841
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased3100wt: 0.39 / mu: 0.56wt: GATGGCCCGCCATCTGCGCGAGTACCAGGACCTGCTCAACG
mu: GATGGCCCGCCATCTGCGCGAGTACCCGGACCTGCTCAACG
 gcga|GTAC
distance from splice site 79
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      389KDEMARHLREYQDLLNVKMALDVE
mutated  not conserved    389KDEMARHLREYPDLLNVKMALDV
Ptroglodytes  all identical  ENSPTRG00000012955  389KDEMARHLREYQDLLNVKMALDV
Mmulatta  all identical  ENSMMUG00000017933  389KDEMARHLREYQDLLNVKMALDV
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000026208  388KDEMARHLREYQDLLNVKMALDV
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000019275  377KDEMARHLREYQDLLNVKMALDV
protein features
start (aa)end (aa)featuredetails 
109412REGIONRod.lost
296412REGIONCoil 2B.lost
413470REGIONTail.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1413 / 1413
position (AA) of stopcodon in wt / mu AA sequence 471 / 471
position of stopcodon in wt / mu cDNA 1499 / 1499
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 87 / 87
chromosome 2
strand 1
last intron/exon boundary 1458
theoretical NMD boundary in CDS 1321
length of CDS 1413
coding sequence (CDS) position 1166
cDNA position
(for ins/del: last normal base / first normal base)
1252
gDNA position
(for ins/del: last normal base / first normal base)
3106
chromosomal position
(for ins/del: last normal base / first normal base)
220286204
original gDNA sequence snippet CCGCCATCTGCGCGAGTACCAGGACCTGCTCAACGTGAAGA
altered gDNA sequence snippet CCGCCATCTGCGCGAGTACCCGGACCTGCTCAACGTGAAGA
original cDNA sequence snippet CCGCCATCTGCGCGAGTACCAGGACCTGCTCAACGTGAAGA
altered cDNA sequence snippet CCGCCATCTGCGCGAGTACCCGGACCTGCTCAACGTGAAGA
wildtype AA sequence MSQAYSSSQR VSSYRRTFGG APGFPLGSPL SSPVFPRAGF GSKGSSSSVT SRVYQVSRTS
GGAGGLGSLR ASRLGTTRTP SSYGAGELLD FSLADAVNQE FLTTRTNEKV ELQELNDRFA
NYIEKVRFLE QQNAALAAEV NRLKGREPTR VAELYEEELR ELRRQVEVLT NQRARVDVER
DNLLDDLQRL KAKLQEEIQL KEEAENNLAA FRADVDAATL ARIDLERRIE SLNEEIAFLK
KVHEEEIREL QAQLQEQQVQ VEMDMSKPDL TAALRDIRAQ YETIAAKNIS EAEEWYKSKV
SDLTQAANKN NDALRQAKQE MMEYRHQIQS YTCEIDALKG TNDSLMRQMR ELEDRFASEA
SGYQDNIARL EEEIRHLKDE MARHLREYQD LLNVKMALDV EIATYRKLLE GEESRINLPI
QTYSALNFRE TSPEQRGSEV HTKKTVMIKT IETRDGEVVS EATQQQHEVL *
mutated AA sequence MSQAYSSSQR VSSYRRTFGG APGFPLGSPL SSPVFPRAGF GSKGSSSSVT SRVYQVSRTS
GGAGGLGSLR ASRLGTTRTP SSYGAGELLD FSLADAVNQE FLTTRTNEKV ELQELNDRFA
NYIEKVRFLE QQNAALAAEV NRLKGREPTR VAELYEEELR ELRRQVEVLT NQRARVDVER
DNLLDDLQRL KAKLQEEIQL KEEAENNLAA FRADVDAATL ARIDLERRIE SLNEEIAFLK
KVHEEEIREL QAQLQEQQVQ VEMDMSKPDL TAALRDIRAQ YETIAAKNIS EAEEWYKSKV
SDLTQAANKN NDALRQAKQE MMEYRHQIQS YTCEIDALKG TNDSLMRQMR ELEDRFASEA
SGYQDNIARL EEEIRHLKDE MARHLREYPD LLNVKMALDV EIATYRKLLE GEESRINLPI
QTYSALNFRE TSPEQRGSEV HTKKTVMIKT IETRDGEVVS EATQQQHEVL *
speed 1.30 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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Problems