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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: ENST00000382353
MT speed 0 s - this script 2.399174 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
FGF9disease_causing_automatic0.999994938128757simple_aaeaffected0S99Nsingle base exchangers121918322show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.999994938128757 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM094242)
  • known disease mutation: rs8705 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr13:22255199G>AN/A show variant in all transcripts   IGV
HGNC symbol FGF9
Ensembl transcript ID ENST00000382353
Genbank transcript ID NM_002010
UniProt peptide P31371
alteration type single base exchange
alteration region CDS
DNA changes c.296G>A
cDNA.826G>A
g.9678G>A
AA changes S99N Score: 46 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 99
frameshift no
known variant Reference ID: rs121918322
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs8705 (pathogenic for Multiple synostoses syndrome 3) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM094242)

known disease mutation at this position, please check HGMD for details (HGMD ID CM094242)
known disease mutation at this position, please check HGMD for details (HGMD ID CM094242)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)4.7351
5.721
(flanking)1.5731
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 increased9682wt: 0.9131 / mu: 0.9172 (marginal change - not scored)wt: AGTATAGCAGTGGGC
mu: AATATAGCAGTGGGC		 TATA|gcag
Donor gained96800.33mu: TCAATATAGCAGTGG AATA|tagc
distance from splice site 19
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      99DHSRFGILEFISIAVGLVSIRGVD
mutated  all conserved    99DHSRFGILEFINIAVGLVSIRGV
Ptroglodytes  all identical  ENSPTRG00000005698  99DHSRFGILEFISIAVGLVSIRGV
Mmulatta  all identical  ENSMMUG00000009912  99SDSKHGILEFISIAVGLVSIRGV
Fcatus  all identical  ENSFCAG00000005991  99DHSRFGILEFISIAVGLVSIRGV
Mmusculus  all identical  ENSMUSG00000021974  99DHSRFGILEFISIAVGLVSIRGV
Ggallus  not conserved  ENSGALG00000017124  99DHSRFGSLFVVPLGMGQMVVGGV
Trubripes  no homologue    
Drerio  no homologue    
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000021075  99DHNRFGILEFISIAVGLVSIRGV
protein features
start (aa)end (aa)featuredetails 
95101STRANDlost
104109STRANDmight get lost (downstream of altered splice site)
110112TURNmight get lost (downstream of altered splice site)
115118STRANDmight get lost (downstream of altered splice site)
124129STRANDmight get lost (downstream of altered splice site)
132134HELIXmight get lost (downstream of altered splice site)
136142STRANDmight get lost (downstream of altered splice site)
145154STRANDmight get lost (downstream of altered splice site)
156158TURNmight get lost (downstream of altered splice site)
161163STRANDmight get lost (downstream of altered splice site)
175177HELIXmight get lost (downstream of altered splice site)
183185HELIXmight get lost (downstream of altered splice site)
187190STRANDmight get lost (downstream of altered splice site)
194196HELIXmight get lost (downstream of altered splice site)
200203HELIXmight get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 627 / 627
position (AA) of stopcodon in wt / mu AA sequence 209 / 209
position of stopcodon in wt / mu cDNA 1157 / 1157
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 531 / 531
chromosome 13
strand 1
last intron/exon boundary 912
theoretical NMD boundary in CDS 331
length of CDS 627
coding sequence (CDS) position 296
cDNA position
(for ins/del: last normal base / first normal base)		 826
gDNA position
(for ins/del: last normal base / first normal base)		 9678
chromosomal position
(for ins/del: last normal base / first normal base)		 22255199
original gDNA sequence snippet AGGCATTCTGGAATTTATCAGTATAGCAGTGGGCCTGGTCA
altered gDNA sequence snippet AGGCATTCTGGAATTTATCAATATAGCAGTGGGCCTGGTCA
original cDNA sequence snippet TGGCATTCTGGAATTTATCAGTATAGCAGTGGGCCTGGTCA
altered cDNA sequence snippet TGGCATTCTGGAATTTATCAATATAGCAGTGGGCCTGGTCA
wildtype AA sequence MAPLGEVGNY FGVQDAVPFG NVPVLPVDSP VLLSDHLGQS EAGGLPRGPA VTDLDHLKGI
LRRRQLYCRT GFHLEIFPNG TIQGTRKDHS RFGILEFISI AVGLVSIRGV DSGLYLGMNE
KGELYGSEKL TQECVFREQF EENWYNTYSS NLYKHVDTGR RYYVALNKDG TPREGTRTKR
HQKFTHFLPR PVDPDKVPEL YKDILSQS*
mutated AA sequence MAPLGEVGNY FGVQDAVPFG NVPVLPVDSP VLLSDHLGQS EAGGLPRGPA VTDLDHLKGI
LRRRQLYCRT GFHLEIFPNG TIQGTRKDHS RFGILEFINI AVGLVSIRGV DSGLYLGMNE
KGELYGSEKL TQECVFREQF EENWYNTYSS NLYKHVDTGR RYYVALNKDG TPREGTRTKR
HQKFTHFLPR PVDPDKVPEL YKDILSQS*
speed 0.35 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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Problems