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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 2.22 s - this script 5.815816 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
DESdisease_causing_automatic0.999923491600308simple_aae0A337Psingle base exchangers59962885show file

Taster files

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Prediction

disease causing

Model: simple_aae, prob: 0.999923491600308 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM980537)
  • known disease mutation: rs16820 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:220285661G>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.1009G>C
cDNA.1095G>C
g.2563G>C
AA changes A337P Score: 27 explain score(s)
position(s) of altered AA
if AA alteration in CDS
337
frameshift no
known variant Reference ID: rs59962885
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs16820 (pathogenic for Myofibrillar myopathy 1|Dilated cardiomyopathy 1I|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM980537)

known disease mutation at this position, please check HGMD for details (HGMD ID CM980537)
known disease mutation at this position, please check HGMD for details (HGMD ID CM980537)
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
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.8010.548
3.510.998
(flanking)5.8031
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor marginally increased2567wt: 0.6287 / mu: 0.6672 (marginal change - not scored)wt: CGCCCTGAAGGGCAC
mu: CCCCCTGAAGGGCAC
 CCCT|gaag
distance from splice site 15
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      337HQIQSYTCEIDALKGTNDSLMRQM
mutated  not conserved    337HQIQSYTCEIDPLKGTNDSLMRQ
Ptroglodytes  all identical  ENSPTRG00000012955  337HQIQSYTCEIDALKGTNDSLMRQ
Mmulatta  all identical  ENSMMUG00000017933  337HQIQSYTCEIDALKGTNDSLMRQ
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000026208  336HQIQSYTCEIDALKGTNDSLMRQ
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000019275  325HQIQSYTCEIDALKGTNDSLMRQ
protein features
start (aa)end (aa)featuredetails 
109412REGIONRod.lost
296412REGIONCoil 2B.lost
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 1009
cDNA position
(for ins/del: last normal base / first normal base)
1095
gDNA position
(for ins/del: last normal base / first normal base)
2563
chromosomal position
(for ins/del: last normal base / first normal base)
220285661
original gDNA sequence snippet CCTACACCTGCGAGATTGACGCCCTGAAGGGCACTGTGAGT
altered gDNA sequence snippet CCTACACCTGCGAGATTGACCCCCTGAAGGGCACTGTGAGT
original cDNA sequence snippet CCTACACCTGCGAGATTGACGCCCTGAAGGGCACTAACGAT
altered cDNA sequence snippet CCTACACCTGCGAGATTGACCCCCTGAAGGGCACTAACGAT
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 YTCEIDPLKG TNDSLMRQMR ELEDRFASEA
SGYQDNIARL EEEIRHLKDE MARHLREYQD LLNVKMALDV EIATYRKLLE GEESRINLPI
QTYSALNFRE TSPEQRGSEV HTKKTVMIKT IETRDGEVVS EATQQQHEVL *
speed 2.22 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