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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: ENST00000264664
MT speed 0.63 s - this script 2.720951 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
FGF10disease_causing_automatic0.999808400153773simple_aaeaffected0R80Ssingle base exchangers104893888show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.999808400153773 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM070926)
  • known disease mutation: rs7534 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:44388545T>GN/A show variant in all transcripts   IGV
HGNC symbol FGF10
Ensembl transcript ID ENST00000264664
Genbank transcript ID NM_004465
UniProt peptide O15520
alteration type single base exchange
alteration region CDS
DNA changes c.240A>C
cDNA.355A>C
g.1264A>C
AA changes R80S Score: 110 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 80
frameshift no
known variant Reference ID: rs104893888
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs7534 (pathogenic for Levy-Hollister syndrome|Congenital absence of salivary gland) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM070926)

known disease mutation at this position, please check HGMD for details (HGMD ID CM070926)
known disease mutation at this position, please check HGMD for details (HGMD ID CM070926)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K4me2, Histone, Histone 3 Lysine 4 Di-Methylation
H3K4me3, Histone, Histone 3 Lysine 4 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.1391
0.3860.999
(flanking)5.8271
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased1266wt: 0.56 / mu: 0.65wt: GAGAAAGCTATTCTC
mu: GAGCAAGCTATTCTC		 GAAA|gcta
Donor marginally increased1262wt: 0.8345 / mu: 0.8666 (marginal change - not scored)wt: GCTGGAGAAAGCTAT
mu: GCTGGAGCAAGCTAT		 TGGA|gaaa
distance from splice site 86
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      80SYNHLQGDVRWRKLFSFTKYFLKI
mutated  not conserved    80SYNHLQGDVRWSKLFSFTKYFLK
Ptroglodytes  all identical  ENSPTRG00000016853  80SYNHLQGDVRWRKLFSFTKYFLK
Mmulatta  all identical  ENSMMUG00000015527  80SYNHLQGDVRWRKLFSFTKYFLK
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000021732  81SYNHLQGDVRWRRLFSFTKYFLT
Ggallus  no alignment  ENSGALG00000014872  n/a
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000030932  76SYNHLTGDVRRRKLFSYQKFFLR
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000025130  117SYNHLQGDVRSRKLFSYTKYFLQ
protein features
start (aa)end (aa)featuredetails 
7684STRANDlost
8992STRANDmight get lost (downstream of altered splice site)
98101STRANDmight get lost (downstream of altered splice site)
111117STRANDmight get lost (downstream of altered splice site)
120120CONFLICTV -> A (in Ref. 3; AAL05875).might get lost (downstream of altered splice site)
120125STRANDmight get lost (downstream of altered splice site)
126129TURNmight get lost (downstream of altered splice site)
130134STRANDmight get lost (downstream of altered splice site)
134134CONFLICTM -> R (in Ref. 3; AAL05875).might get lost (downstream of altered splice site)
138145STRANDmight get lost (downstream of altered splice site)
150156STRANDmight get lost (downstream of altered splice site)
162171STRANDmight get lost (downstream of altered splice site)
174177STRANDmight get lost (downstream of altered splice site)
189191HELIXmight get lost (downstream of altered splice site)
196196CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
197199HELIXmight get lost (downstream of altered splice site)
201205STRANDmight 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 742 / 742
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 5
strand -1
last intron/exon boundary 545
theoretical NMD boundary in CDS 379
length of CDS 627
coding sequence (CDS) position 240
cDNA position
(for ins/del: last normal base / first normal base)		 355
gDNA position
(for ins/del: last normal base / first normal base)		 1264
chromosomal position
(for ins/del: last normal base / first normal base)		 44388545
original gDNA sequence snippet CAAGGAGATGTCCGCTGGAGAAAGCTATTCTCTTTCACCAA
altered gDNA sequence snippet CAAGGAGATGTCCGCTGGAGCAAGCTATTCTCTTTCACCAA
original cDNA sequence snippet CAAGGAGATGTCCGCTGGAGAAAGCTATTCTCTTTCACCAA
altered cDNA sequence snippet CAAGGAGATGTCCGCTGGAGCAAGCTATTCTCTTTCACCAA
wildtype AA sequence MWKWILTHCA SAFPHLPGCC CCCFLLLFLV SSVPVTCQAL GQDMVSPEAT NSSSSSFSSP
SSAGRHVRSY NHLQGDVRWR KLFSFTKYFL KIEKNGKVSG TKKENCPYSI LEITSVEIGV
VAVKAINSNY YLAMNKKGKL YGSKEFNNDC KLKERIEENG YNTYASFNWQ HNGRQMYVAL
NGKGAPRRGQ KTRRKNTSAH FLPMVVHS*
mutated AA sequence MWKWILTHCA SAFPHLPGCC CCCFLLLFLV SSVPVTCQAL GQDMVSPEAT NSSSSSFSSP
SSAGRHVRSY NHLQGDVRWS KLFSFTKYFL KIEKNGKVSG TKKENCPYSI LEITSVEIGV
VAVKAINSNY YLAMNKKGKL YGSKEFNNDC KLKERIEENG YNTYASFNWQ HNGRQMYVAL
NGKGAPRRGQ KTRRKNTSAH FLPMVVHS*
speed 0.63 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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