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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 1.59 s - this script 5.848127 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
DESdisease_causing_automatic0.999999996649266simple_aae0L345Psingle base exchangers57639980show file

Taster files

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Prediction

disease causing

Model: simple_aae, prob: 0.999999996649266 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM992621)
  • known disease mutation: rs16825 (pathogenic)
  • protein features (might be) affected
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr2:220286072T>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.1034T>C
cDNA.1120T>C
g.2974T>C
AA changes L345P Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS
345
frameshift no
known variant Reference ID: rs57639980
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs16825 (pathogenic for Myofibrillar myopathy 1|Muscular dystrophy, limb-girdle, type 2R|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM992621)

known disease mutation at this position, please check HGMD for details (HGMD ID CM992621)
known disease mutation at this position, please check HGMD for details (HGMD ID CM992621)
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
phyloP / phastCons
PhyloPPhastCons
(flanking)0.9430.981
4.4181
(flanking)2.9231
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 increased2979wt: 0.8885 / mu: 0.8986 (marginal change - not scored)wt: TGATGAGGCAGATGC
mu: CGATGAGGCAGATGC
 ATGA|ggca
Donor marginally increased2972wt: 0.2702 / mu: 0.3100 (marginal change - not scored)wt: GATTCCCTGATGAGG
mu: GATTCCCCGATGAGG
 TTCC|ctga
Donor marginally increased2974wt: 0.9894 / mu: 0.9937 (marginal change - not scored)wt: TTCCCTGATGAGGCA
mu: TTCCCCGATGAGGCA
 CCCT|gatg
distance from splice site 11
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      345EIDALKGTNDSLMRQMRELEDRFA
mutated  not conserved    345EIDALKGTNDSPMRQMRELEDRF
Ptroglodytes  all identical  ENSPTRG00000012955  345EIDALKGTNDSLMRQMRELEDRF
Mmulatta  all identical  ENSMMUG00000017933  345EIDALKGTNDSLMRQMRELEDRF
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000026208  344EIDALKGTNDSLMRQMRELEDRF
Ggallus  no homologue    
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000019275  333EIDALKGTNDSLMRQMRDLEERF
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 1034
cDNA position
(for ins/del: last normal base / first normal base)
1120
gDNA position
(for ins/del: last normal base / first normal base)
2974
chromosomal position
(for ins/del: last normal base / first normal base)
220286072
original gDNA sequence snippet TCTCCTGCAGAACGATTCCCTGATGAGGCAGATGCGGGAAT
altered gDNA sequence snippet TCTCCTGCAGAACGATTCCCCGATGAGGCAGATGCGGGAAT
original cDNA sequence snippet GAAGGGCACTAACGATTCCCTGATGAGGCAGATGCGGGAAT
altered cDNA sequence snippet GAAGGGCACTAACGATTCCCCGATGAGGCAGATGCGGGAAT
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 TNDSPMRQMR ELEDRFASEA
SGYQDNIARL EEEIRHLKDE MARHLREYQD LLNVKMALDV EIATYRKLLE GEESRINLPI
QTYSALNFRE TSPEQRGSEV HTKKTVMIKT IETRDGEVVS EATQQQHEVL *
speed 1.59 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