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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: ENST00000271651
MT speed 0 s - this script 2.582043 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
CTSKdisease_causing_automatic0.999999932772223simple_aaeaffected0G79Esingle base exchangers74315305show file

Taster files

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 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999932772223 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM990445)
  • known disease mutation: rs8424 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:150778585C>TN/A show variant in all transcripts   IGV
HGNC symbol CTSK
Ensembl transcript ID ENST00000271651
Genbank transcript ID NM_000396
UniProt peptide P43235
alteration type single base exchange
alteration region CDS
DNA changes c.236G>A
cDNA.347G>A
g.2215G>A
AA changes G79E Score: 98 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 79
frameshift no
known variant Reference ID: rs74315305
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs8424 (pathogenic for Pyknodysostosis) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM990445)

known disease mutation at this position, please check HGMD for details (HGMD ID CM990445)
known disease mutation at this position, please check HGMD for details (HGMD ID CM990445)
regulatory features H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.4540.93
3.9491
(flanking)3.9411
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased2216wt: 0.54 / mu: 0.87wt: CTGGGGGACATGGCA
mu: CTGGAGGACATGGCA		 GGGG|gaca
Donor gained22100.91mu: AACCACCTGGAGGAC CCAC|ctgg
distance from splice site 8
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      79VHTYELAMNHLGDMTSEEVVQKMT
mutated  not conserved    79VHTYELAMNHLEDMTSEEVVQKM
Ptroglodytes  all identical  ENSPTRG00000001265  79VHTYELAMNHLGDMTSEEVVQKM
Mmulatta  all identical  ENSMMUG00000000537  79VHTYELAMNHLGDMTNEEVVQKM
Fcatus  all identical  ENSFCAG00000003643  80VHTYELAMNHLGDMTSEEVVQKM
Mmusculus  all identical  ENSMUSG00000028111  79VHTYELAMNHLGDMTSEEVVQKM
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000000525  81MHSYELGMNHLGDMVSPSRTSEEVLEKM
Drerio  all identical  ENSDARG00000040251  83IHTYDLGMNHFGDM
Dmelanogaster  not conserved  FBgn0013770  112KVSFKLAVNKYADLLHHEFRQLM
Celegans  not conserved  T03E6.7  85RKTFEMGLNHIADLPFSQ
Xtropicalis  all identical  ENSXETG00000008929  81LHTYDLAMNHLGDMMTPYRPLANQ
protein features
start (aa)end (aa)featuredetails 
16114PROPEPActivation peptide. /FTId=PRO_0000026295.lost
7981STRANDlost
8389HELIXmight get lost (downstream of altered splice site)
102107STRANDmight get lost (downstream of altered splice site)
103103CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
121125TURNmight get lost (downstream of altered splice site)
135137STRANDmight get lost (downstream of altered splice site)
136136DISULFIDmight get lost (downstream of altered splice site)
139139ACT_SITEBy similarity.might get lost (downstream of altered splice site)
139156HELIXmight get lost (downstream of altered splice site)
164170HELIXmight get lost (downstream of altered splice site)
170170DISULFIDmight get lost (downstream of altered splice site)
176178HELIXmight get lost (downstream of altered splice site)
177177DISULFIDmight get lost (downstream of altered splice site)
182192HELIXmight get lost (downstream of altered splice site)
195197STRANDmight get lost (downstream of altered splice site)
198200TURNmight get lost (downstream of altered splice site)
210210DISULFIDmight get lost (downstream of altered splice site)
214216HELIXmight get lost (downstream of altered splice site)
217219STRANDmight get lost (downstream of altered splice site)
224226STRANDmight get lost (downstream of altered splice site)
232241HELIXmight get lost (downstream of altered splice site)
245249STRANDmight get lost (downstream of altered splice site)
254257HELIXmight get lost (downstream of altered splice site)
261264STRANDmight get lost (downstream of altered splice site)
269269DISULFIDmight get lost (downstream of altered splice site)
276276ACT_SITEBy similarity.might get lost (downstream of altered splice site)
276286STRANDmight get lost (downstream of altered splice site)
289295STRANDmight get lost (downstream of altered splice site)
296296ACT_SITEBy similarity.might get lost (downstream of altered splice site)
300302STRANDmight get lost (downstream of altered splice site)
303305TURNmight get lost (downstream of altered splice site)
307316STRANDmight get lost (downstream of altered splice site)
317319HELIXmight get lost (downstream of altered splice site)
318318DISULFIDmight get lost (downstream of altered splice site)
320322TURNmight get lost (downstream of altered splice site)
325327STRANDmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 990 / 990
position (AA) of stopcodon in wt / mu AA sequence 330 / 330
position of stopcodon in wt / mu cDNA 1101 / 1101
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 112 / 112
chromosome 1
strand -1
last intron/exon boundary 1002
theoretical NMD boundary in CDS 840
length of CDS 990
coding sequence (CDS) position 236
cDNA position
(for ins/del: last normal base / first normal base)		 347
gDNA position
(for ins/del: last normal base / first normal base)		 2215
chromosomal position
(for ins/del: last normal base / first normal base)		 150778585
original gDNA sequence snippet ACTGGCTATGAACCACCTGGGGGACATGGCAAGTATAGCTT
altered gDNA sequence snippet ACTGGCTATGAACCACCTGGAGGACATGGCAAGTATAGCTT
original cDNA sequence snippet ACTGGCTATGAACCACCTGGGGGACATGACCAGTGAAGAGG
altered cDNA sequence snippet ACTGGCTATGAACCACCTGGAGGACATGACCAGTGAAGAGG
wildtype AA sequence MWGLKVLLLP VVSFALYPEE ILDTHWELWK KTHRKQYNNK VDEISRRLIW EKNLKYISIH
NLEASLGVHT YELAMNHLGD MTSEEVVQKM TGLKVPLSHS RSNDTLYIPE WEGRAPDSVD
YRKKGYVTPV KNQGQCGSCW AFSSVGALEG QLKKKTGKLL NLSPQNLVDC VSENDGCGGG
YMTNAFQYVQ KNRGIDSEDA YPYVGQEESC MYNPTGKAAK CRGYREIPEG NEKALKRAVA
RVGPVSVAID ASLTSFQFYS KGVYYDESCN SDNLNHAVLA VGYGIQKGNK HWIIKNSWGE
NWGNKGYILM ARNKNNACGI ANLASFPKM*
mutated AA sequence MWGLKVLLLP VVSFALYPEE ILDTHWELWK KTHRKQYNNK VDEISRRLIW EKNLKYISIH
NLEASLGVHT YELAMNHLED MTSEEVVQKM TGLKVPLSHS RSNDTLYIPE WEGRAPDSVD
YRKKGYVTPV KNQGQCGSCW AFSSVGALEG QLKKKTGKLL NLSPQNLVDC VSENDGCGGG
YMTNAFQYVQ KNRGIDSEDA YPYVGQEESC MYNPTGKAAK CRGYREIPEG NEKALKRAVA
RVGPVSVAID ASLTSFQFYS KGVYYDESCN SDNLNHAVLA VGYGIQKGNK HWIIKNSWGE
NWGNKGYILM ARNKNNACGI ANLASFPKM*
speed 0.38 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

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