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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 3.374706 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CTSCdisease_causing0.999999999961453simple_aaeaffectedQ252Lsingle base exchangers104894207show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.999999999961453      (explain)
Summary
  • amino acid sequence changed
  • known as potential disease variant: rs7291 (probable pathogenic)
  • known disease mutation at this position (HGMD CM993133)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:88033700T>AN/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.755A>T
cDNA.870A>T
g.37256A>T
AA changes Q252L Score: 113 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 252
frameshift no
known variant Reference ID: rs104894207
Allele 'A' was neither found in ExAC nor 1000G.
known as potential disease variant: rs7291 (probable pathogenic for Papillon-Lefèvre syndrome|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM993133)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993133)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993133)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.351
4.851
(flanking)5.8741
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost37258sequence motif lost- wt: CAAG|gtaa
 mu: CTAG.gtaa
Donor marginally decreased37258wt: 0.9938 / mu: 0.9835 (marginal change - not scored)wt: ACCAAGGTAAAAAAA
mu: ACCTAGGTAAAAAAA		 CAAG|gtaa
Donor gained372490.53mu: CTGTTCGAAACCTAG GTTC|gaaa
distance from splice site 3
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      252HGINFVSPVRNQASCGSCYSFASM
mutated  not conserved    252HGINFVSPVRNLASCGSCYSFAS
Ptroglodytes  all identical  ENSPTRG00000004152  252HGINFVSPVRNQASCGSCYSFAS
Mmulatta  all identical  ENSMMUG00000022139  252HGINFVSPVRNQASCGSCYSFAS
Fcatus  all identical  ENSFCAG00000008445  252HGTNFVTPVRNQASCGSCYSFAS
Mmusculus  all identical  ENSMUSG00000030560  251QGVNYVSPVRNQESCGSCYSFAS
Ggallus  all identical  ENSGALG00000017239  252PVRNQASCGSCYAFAS
Trubripes  all identical  ENSTRUG00000006734  252VNFVSPVRNQGSCGSCYCFAT
Drerio  all identical  ENSDARG00000018806  245VRNQAQCGSCYSFAT
Dmelanogaster  no homologue    
Celegans  all identical  F15D4.4  245----FLKPILDQSTCGGCWAFSM
Xtropicalis  all identical  ENSXETG00000011748  247YNFVTPVRNQASCGSCYAFSS
protein features
start (aa)end (aa)featuredetails 
255255DISULFIDmight get lost (downstream of altered splice site)
258258ACT_SITEmight get lost (downstream of altered splice site)
258275HELIXmight get lost (downstream of altered splice site)
276276CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
285291HELIXmight get lost (downstream of altered splice site)
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)
321321DISULFIDmight get lost (downstream of altered splice site)
321321CONFLICTC -> S (in Ref. 14; AA sequence).might 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 755
cDNA position
(for ins/del: last normal base / first normal base)		 870
gDNA position
(for ins/del: last normal base / first normal base)		 37256
chromosomal position
(for ins/del: last normal base / first normal base)		 88033700
original gDNA sequence snippet TGTCAGTCCTGTTCGAAACCAAGGTAAAAAAATAAGCCTAA
altered gDNA sequence snippet TGTCAGTCCTGTTCGAAACCTAGGTAAAAAAATAAGCCTAA
original cDNA sequence snippet TGTCAGTCCTGTTCGAAACCAAGCATCCTGTGGCAGCTGCT
altered cDNA sequence snippet TGTCAGTCCTGTTCGAAACCTAGCATCCTGTGGCAGCTGCT
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 NLASCGSCYS FASMGMLEAR IRILTNNSQT PILSPQEVVS CSQYAQGCEG
GFPYLIAGKY AQDFGLVEEA CFPYTGTDSP CKMKEDCFRY YSSEYHYVGG FYGGCNEALM
KLELVHHGPM AVAFEVYDDF LHYKKGIYHH TGLRDPFNPF ELTNHAVLLV GYGTDSASGM
DYWIVKNSWG TGWGENGYFR IRRGTDECAI ESIAVAATPI PKL*
speed 1.22 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
back to results table

Problems