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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 3.730563 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CTSCdisease_causing_automatic0.999999999941376simple_aaeaffected0Q286Rsingle base exchangers104894208show file

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Prediction

disease causing

Model: simple_aae, prob: 0.999999999941376 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM000135)
  • known disease mutation: rs7294 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:88029333T>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.857A>G
cDNA.972A>G
g.41623A>G
AA changes Q286R Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS
286
frameshift no
known variant Reference ID: rs104894208
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs7294 (pathogenic for Haim-Munk syndrome|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM000135)

known disease mutation at this position, please check HGMD for details (HGMD ID CM000135)
known disease mutation at this position, please check HGMD for details (HGMD ID CM000135)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)1.9651
5.1181
(flanking)6.1991
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased41616wt: 0.35 / mu: 0.46wt: ATTCTCAGACCCCAATCCTAAGCCCTCAGGAGGTTGTGTCT
mu: ATTCTCAGACCCCAATCCTAAGCCCTCGGGAGGTTGTGTCT
 ctaa|GCCC
Donor gained416220.89mu: GCCCTCGGGAGGTTG CCTC|ggga
distance from splice site 33
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      286TNNSQTPILSPQEVVSCSQYAQGC
mutated  all conserved    286TNNSQTPILSPREVVSCSQYAQG
Ptroglodytes  all identical  ENSPTRG00000004152  286TNNSQTPILSPQEVVSCSQYAQG
Mmulatta  all identical  ENSMMUG00000022139  286TNNSQTPILSPQEVVSCSQYAQG
Fcatus  all identical  ENSFCAG00000008445  286TNNTQTPILSPQEVVSCSQYAQG
Mmusculus  all identical  ENSMUSG00000030560  285TNNSQTPILSPQEVVSCSPYAQG
Ggallus  all identical  ENSGALG00000017239  286TNNTQKPVFSPQQVVSCSQYSQG
Trubripes  all identical  ENSTRUG00000006734  286TNNSQSPVLSPQQVVSCSEYSQG
Drerio  all identical  ENSDARG00000018806  279TNNTQQPVFSPQQVVSCSQYSQG
Dmelanogaster  no homologue    
Celegans  all identical  F15D4.4  273GYNTSS--LSVQQLLTCDTKVDSTYGLANVG
Xtropicalis  all identical  ENSXETG00000011748  281SQLSQKPILSPQQVVSCSNYSQG
protein features
start (aa)end (aa)featuredetails 
285291HELIXlost
291291DISULFIDmight get lost (downstream of altered splice site)
298298DISULFIDmight get lost (downstream of altered splice site)
302302BINDINGChloride.might get lost (downstream of altered splice site)
303306HELIXmight get lost (downstream of altered splice site)
304304BINDINGChloride; via amide nitrogen.might get lost (downstream of altered splice site)
309313HELIXmight get lost (downstream of altered splice site)
319321HELIXmight get lost (downstream of altered splice site)
321321CONFLICTC -> S (in Ref. 14; AA sequence).might get lost (downstream of altered splice site)
321321DISULFIDmight get lost (downstream of altered splice site)
331331DISULFIDmight get lost (downstream of altered splice site)
337337DISULFIDmight get lost (downstream of altered splice site)
342347STRANDmight get lost (downstream of altered splice site)
347347BINDINGChloride.might get lost (downstream of altered splice site)
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 857
cDNA position
(for ins/del: last normal base / first normal base)
972
gDNA position
(for ins/del: last normal base / first normal base)
41623
chromosomal position
(for ins/del: last normal base / first normal base)
88029333
original gDNA sequence snippet GACCCCAATCCTAAGCCCTCAGGAGGTTGTGTCTTGTAGCC
altered gDNA sequence snippet GACCCCAATCCTAAGCCCTCGGGAGGTTGTGTCTTGTAGCC
original cDNA sequence snippet GACCCCAATCCTAAGCCCTCAGGAGGTTGTGTCTTGTAGCC
altered cDNA sequence snippet GACCCCAATCCTAAGCCCTCGGGAGGTTGTGTCTTGTAGCC
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 PILSPREVVS CSQYAQGCEG
GFPYLIAGKY AQDFGLVEEA CFPYTGTDSP CKMKEDCFRY YSSEYHYVGG FYGGCNEALM
KLELVHHGPM AVAFEVYDDF LHYKKGIYHH TGLRDPFNPF ELTNHAVLLV GYGTDSASGM
DYWIVKNSWG TGWGENGYFR IRRGTDECAI ESIAVAATPI PKL*
speed 1.66 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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