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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: ENST00000227266
MT speed 0 s - this script 2.888678 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CTSCdisease_causing_automatic0.999999999999937simple_aaeaffected0Y347Csingle base exchangers104894211show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.999999999999937 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM993138)
  • known disease mutation: rs7301 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:88027526T>CN/A show variant in all transcripts   IGV
HGNC symbol CTSC
Ensembl transcript ID ENST00000227266
Genbank transcript ID NM_001814
UniProt peptide P53634
alteration type single base exchange
alteration region CDS
DNA changes c.1040A>G
cDNA.1155A>G
g.43430A>G
AA changes Y347C Score: 194 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 347
frameshift no
known variant Reference ID: rs104894211
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs7301 (pathogenic for Periodontitis, aggressive, 1|Papillon-Lefèvre syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM993138)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993138)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993138)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me1, Histone, Histone 3 Lysine 27 mono-methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)0.0360.99
5.3061
(flanking)5.3061
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased43423wt: 0.28 / mu: 0.40wt: TTCGTTATTACTCCTCTGAGTACCACTATGTAGGAGGTTTC
mu: TTCGTTATTACTCCTCTGAGTACCACTGTGTAGGAGGTTTC		 gagt|ACCA
Acc marginally increased43421wt: 0.9887 / mu: 0.9923 (marginal change - not scored)wt: CTTTCGTTATTACTCCTCTGAGTACCACTATGTAGGAGGTT
mu: CTTTCGTTATTACTCCTCTGAGTACCACTGTGTAGGAGGTT		 ctga|GTAC
Donor gained434290.92mu: ACCACTGTGTAGGAG CACT|gtgt
distance from splice site 151
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      347DCFRYYSSEYHYVGGFYGGCNEAL
mutated  not conserved    347DCFRYYSSEYHCVGGFYGGCNEA
Ptroglodytes  all identical  ENSPTRG00000004152  347DCFRYYSSEYHYVGGFYGGCNEA
Mmulatta  all identical  ENSMMUG00000022139  347DCFRYYSSEYHYVGGFYGGCNEA
Fcatus  all identical  ENSFCAG00000008445  347DCVRYYSSEYHYVGGFYGGCNEA
Mmusculus  all identical  ENSMUSG00000030560  346NCLRYYSSDYYYVGGFYGGCNEA
Ggallus  all identical  ENSGALG00000017239  347SCYHYYTSEYHYVGGFYGACNEA
Trubripes  all identical  ENSTRUG00000006734  347SCRRGYAAEYKYVGGFYGGCSEA
Drerio  all identical  ENSDARG00000018806  339KCTKYYASDYHYVGGFYGGCSES
Dmelanogaster  no homologue    
Celegans  all identical  F15D4.4  339SSFFPPVVPTILLFDDGYISGNFTAAQLI
Xtropicalis  all identical  ENSXETG00000011748  342SQQKYYTAEYHYVGGFYGGCNEA
protein features
start (aa)end (aa)featuredetails 
342347STRANDlost
347347BINDINGChloride.lost
355355CONFLICTC -> M (in Ref. 14; AA sequence).might get lost (downstream of altered splice site)
357367HELIXmight get lost (downstream of altered splice site)
366366CONFLICTH -> R (in Ref. 14; AA sequence).might get lost (downstream of altered splice site)
370374STRANDmight get lost (downstream of altered splice site)
376378CONFLICTVYD -> YVY (in Ref. 14; AA sequence).might get lost (downstream of altered splice site)
378382HELIXmight get lost (downstream of altered splice site)
385388STRANDmight get lost (downstream of altered splice site)
405405ACT_SITEmight get lost (downstream of altered splice site)
405414STRANDmight get lost (downstream of altered splice site)
416418TURNmight get lost (downstream of altered splice site)
421426STRANDmight get lost (downstream of altered splice site)
427427ACT_SITEmight get lost (downstream of altered splice site)
438442STRANDmight get lost (downstream of altered splice site)
447449HELIXmight get lost (downstream of altered splice site)
455459STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1392 / 1392
position (AA) of stopcodon in wt / mu AA sequence 464 / 464
position of stopcodon in wt / mu cDNA 1507 / 1507
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 116 / 116
chromosome 11
strand -1
last intron/exon boundary 1005
theoretical NMD boundary in CDS 839
length of CDS 1392
coding sequence (CDS) position 1040
cDNA position
(for ins/del: last normal base / first normal base)		 1155
gDNA position
(for ins/del: last normal base / first normal base)		 43430
chromosomal position
(for ins/del: last normal base / first normal base)		 88027526
original gDNA sequence snippet TTACTCCTCTGAGTACCACTATGTAGGAGGTTTCTATGGAG
altered gDNA sequence snippet TTACTCCTCTGAGTACCACTGTGTAGGAGGTTTCTATGGAG
original cDNA sequence snippet TTACTCCTCTGAGTACCACTATGTAGGAGGTTTCTATGGAG
altered cDNA sequence snippet TTACTCCTCTGAGTACCACTGTGTAGGAGGTTTCTATGGAG
wildtype AA sequence MGAGPSLLLA ALLLLLSGDG AVRCDTPANC TYLDLLGTWV FQVGSSGSQR DVNCSVMGPQ
EKKVVVYLQK LDTAYDDLGN SGHFTIIYNQ GFEIVLNDYK WFAFFKYKEE GSKVTTYCNE
TMTGWVHDVL GRNWACFTGK KVGTASENVY VNIAHLKNSQ EKYSNRLYKY DHNFVKAINA
IQKSWTATTY MEYETLTLGD MIRRSGGHSR KIPRPKPAPL TAEIQQKILH LPTSWDWRNV
HGINFVSPVR NQASCGSCYS FASMGMLEAR IRILTNNSQT PILSPQEVVS CSQYAQGCEG
GFPYLIAGKY AQDFGLVEEA CFPYTGTDSP CKMKEDCFRY YSSEYHYVGG FYGGCNEALM
KLELVHHGPM AVAFEVYDDF LHYKKGIYHH TGLRDPFNPF ELTNHAVLLV GYGTDSASGM
DYWIVKNSWG TGWGENGYFR IRRGTDECAI ESIAVAATPI PKL*
mutated AA sequence MGAGPSLLLA ALLLLLSGDG AVRCDTPANC TYLDLLGTWV FQVGSSGSQR DVNCSVMGPQ
EKKVVVYLQK LDTAYDDLGN SGHFTIIYNQ GFEIVLNDYK WFAFFKYKEE GSKVTTYCNE
TMTGWVHDVL GRNWACFTGK KVGTASENVY VNIAHLKNSQ EKYSNRLYKY DHNFVKAINA
IQKSWTATTY MEYETLTLGD MIRRSGGHSR KIPRPKPAPL TAEIQQKILH LPTSWDWRNV
HGINFVSPVR NQASCGSCYS FASMGMLEAR IRILTNNSQT PILSPQEVVS CSQYAQGCEG
GFPYLIAGKY AQDFGLVEEA CFPYTGTDSP CKMKEDCFRY YSSEYHCVGG FYGGCNEALM
KLELVHHGPM AVAFEVYDDF LHYKKGIYHH TGLRDPFNPF ELTNHAVLLV GYGTDSASGM
DYWIVKNSWG TGWGENGYFR IRRGTDECAI ESIAVAATPI PKL*
speed 0.87 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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