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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 1.44 s - this script 5.605737 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
FGF10disease_causing_automatic0.999515257984353simple_aae0C106Fsingle base exchangers104893885show file

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Prediction

disease causing

Model: simple_aae, prob: 0.999515257984353 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM060992)
  • known disease mutation: rs7531 (pathogenic)
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:44388468C>AN/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.317G>T
cDNA.432G>T
g.1341G>T
AA changes C106F Score: 205 explain score(s)
position(s) of altered AA
if AA alteration in CDS
106
frameshift no
known variant Reference ID: rs104893885
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs7531 (pathogenic for Levy-Hollister syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM060992)

known disease mutation at this position, please check HGMD for details (HGMD ID CM060992)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060992)
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)1.2871
3.5271
(flanking)3.0181
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 increased1344wt: 0.8688 / mu: 0.8798 (marginal change - not scored)wt: CTGCCCGTACAGTAA
mu: CTTCCCGTACAGTAA
 GCCC|gtac
distance from splice site 9
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      106NGKVSGTKKENCPYSILEITSVEI
mutated  not conserved    106NGKVSGTKKENFPYSILEITSVE
Ptroglodytes  all identical  ENSPTRG00000016853  106NGKVSGTKKENCPYSILEITSVE
Mmulatta  all identical  ENSMMUG00000015527  106NGKVSGTKKENCPYSILEITSVE
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000021732  107NGKVSGTKNEDCPYSVLEITSVE
Ggallus  no alignment  ENSGALG00000014872  n/a
Trubripes  no homologue    
Drerio  not conserved  ENSDARG00000030932  102NGKVNGTKSKDDPYSTLEIKSVD
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000025130  143NGTVSGTKKENCPYSILEITSVD
protein features no protein features affected
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 317
cDNA position
(for ins/del: last normal base / first normal base)
432
gDNA position
(for ins/del: last normal base / first normal base)
1341
chromosomal position
(for ins/del: last normal base / first normal base)
44388468
original gDNA sequence snippet CGGGACCAAGAAGGAGAACTGCCCGTACAGTAAGTAACAAA
altered gDNA sequence snippet CGGGACCAAGAAGGAGAACTTCCCGTACAGTAAGTAACAAA
original cDNA sequence snippet CGGGACCAAGAAGGAGAACTGCCCGTACAGCATCCTGGAGA
altered cDNA sequence snippet CGGGACCAAGAAGGAGAACTTCCCGTACAGCATCCTGGAGA
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 NHLQGDVRWR KLFSFTKYFL KIEKNGKVSG TKKENFPYSI LEITSVEIGV
VAVKAINSNY YLAMNKKGKL YGSKEFNNDC KLKERIEENG YNTYASFNWQ HNGRQMYVAL
NGKGAPRRGQ KTRRKNTSAH FLPMVVHS*
speed 1.44 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