Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
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 2.91679 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CTSCdisease_causing_automatic0.999999999999171simple_aaeaffected0G301Ssingle base exchangers104894214show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999999999171 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM993136)
  • known disease mutation: rs7297 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr11:88027665C>TN/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.901G>A
cDNA.1016G>A
g.43291G>A
AA changes G301S Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 301
frameshift no
known variant Reference ID: rs104894214
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC044

known disease mutation: rs7297 (pathogenic for Periodontitis, aggressive, 1|Papillon-Lefèvre syndrome|Haim-Munk syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM993136)

known disease mutation at this position, please check HGMD for details (HGMD ID CM993136)
known disease mutation at this position, please check HGMD for details (HGMD ID CM993136)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)6.4241
6.4241
(flanking)-0.5390.805
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 increased43288wt: 0.2170 / mu: 0.2457 (marginal change - not scored)wt: GTGAAGGCGGCTTCC
mu: GTGAAGGCAGCTTCC		 GAAG|gcgg
Donor marginally increased43282wt: 0.9967 / mu: 0.9967 (marginal change - not scored)wt: CAGGCTGTGAAGGCG
mu: CAGGCTGTGAAGGCA		 GGCT|gtga
Donor gained432870.76mu: TGTGAAGGCAGCTTC TGAA|ggca
distance from splice site 12
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      301SCSQYAQGCEGGFPYLIAGKYAQD
mutated  not conserved    301SFPYLIAGKYAQ
Ptroglodytes  all identical  ENSPTRG00000004152  301GFPYLIAGKYAQ
Mmulatta  all identical  ENSMMUG00000022139  301GFPYLTAGKYAQ
Fcatus  all identical  ENSFCAG00000008445  301GFPYLIAGKYAQ
Mmusculus  all identical  ENSMUSG00000030560  300GFPYLIAGKYAQ
Ggallus  all identical  ENSGALG00000017239  301SCSQYSQGCDGGFPYLIA
Trubripes  all identical  ENSTRUG00000006734  301SCSEYSQGCDGGFPYL-TGKYVQ
Drerio  all identical  ENSDARG00000018806  294SCSQYSQGCDGGFPYLI-G
Dmelanogaster  no homologue    
Celegans  all identical  F15D4.4  288TCDTKVDSTYGLANVGCKGGY-FQIAGSYLE
Xtropicalis  all identical  ENSXETG00000011748  296SCSNYSQGCEGGFPYLIAGKYVS
protein features
start (aa)end (aa)featuredetails 
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 901
cDNA position
(for ins/del: last normal base / first normal base)		 1016
gDNA position
(for ins/del: last normal base / first normal base)		 43291
chromosomal position
(for ins/del: last normal base / first normal base)		 88027665
original gDNA sequence snippet CATCTTCAGGCTGTGAAGGCGGCTTCCCATACCTTATTGCA
altered gDNA sequence snippet CATCTTCAGGCTGTGAAGGCAGCTTCCCATACCTTATTGCA
original cDNA sequence snippet ATGCTCAAGGCTGTGAAGGCGGCTTCCCATACCTTATTGCA
altered cDNA sequence snippet ATGCTCAAGGCTGTGAAGGCAGCTTCCCATACCTTATTGCA
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
SFPYLIAGKY AQDFGLVEEA CFPYTGTDSP CKMKEDCFRY YSSEYHYVGG FYGGCNEALM
KLELVHHGPM AVAFEVYDDF LHYKKGIYHH TGLRDPFNPF ELTNHAVLLV GYGTDSASGM
DYWIVKNSWG TGWGENGYFR IRRGTDECAI ESIAVAATPI PKL*
speed 0.83 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