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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 s - this script 2.895334 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
FGF10disease_causing_automatic0.999999999987518simple_aaeaffected0I156Rsingle base exchangers104893886show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.999999999987518 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM060990)
  • known disease mutation: rs7532 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr5:44305257A>CN/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.467T>G
cDNA.582T>G
g.84552T>G
AA changes I156R Score: 97 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 156
frameshift no
known variant Reference ID: rs104893886
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs7532 (pathogenic for Levy-Hollister syndrome) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM060990)

known disease mutation at this position, please check HGMD for details (HGMD ID CM060990)
known disease mutation at this position, please check HGMD for details (HGMD ID CM060990)
regulatory features N/A
phyloP / phastCons
PhyloPPhastCons
(flanking)1.7771
5.1751
(flanking)5.1751
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased84548wt: 0.85 / mu: 0.97wt: AGGAGAGGATAGAGG
mu: AGGAGAGGAGAGAGG		 GAGA|ggat
Donor marginally increased84544wt: 0.8665 / mu: 0.9012 (marginal change - not scored)wt: CTGAAGGAGAGGATA
mu: CTGAAGGAGAGGAGA		 GAAG|gaga
Donor marginally increased84543wt: 0.9930 / mu: 0.9955 (marginal change - not scored)wt: GCTGAAGGAGAGGAT
mu: GCTGAAGGAGAGGAG		 TGAA|ggag
Donor gained845510.95mu: AGAGGAGAGAGGAAA AGGA|gaga
Donor gained845530.53mu: AGGAGAGAGGAAAAT GAGA|gagg
Donor gained845460.99mu: GAAGGAGAGGAGAGA AGGA|gagg
distance from splice site 38
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      156EFNNDCKLKERIEENGYNTYASFN
mutated  not conserved    156EFNNDCKLKERREENGYNTYASF
Ptroglodytes  all identical  ENSPTRG00000016853  156EFNNDCKLKERIEENGYNTYASF
Mmulatta  all identical  ENSMMUG00000015527  156EFNNDCKLKERIEENGYNTYASF
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000021732  157EFNNDCKLKERIEENGYNTYASF
Ggallus  all identical  ENSGALG00000014872  47EFNSDCKLKAIIEENGYNTYASL
Trubripes  no homologue    
Drerio  all identical  ENSDARG00000030932  150DFGIDCKLIERIEENRYNTYASA
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  all identical  ENSXETG00000025130  193EFNIDCKLKERIEENGYNTYASH
protein features
start (aa)end (aa)featuredetails 
150156STRANDlost
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 467
cDNA position
(for ins/del: last normal base / first normal base)		 582
gDNA position
(for ins/del: last normal base / first normal base)		 84552
chromosomal position
(for ins/del: last normal base / first normal base)		 44305257
original gDNA sequence snippet CTGTAAGCTGAAGGAGAGGATAGAGGAAAATGGATACAATA
altered gDNA sequence snippet CTGTAAGCTGAAGGAGAGGAGAGAGGAAAATGGATACAATA
original cDNA sequence snippet CTGTAAGCTGAAGGAGAGGATAGAGGAAAATGGATACAATA
altered cDNA sequence snippet CTGTAAGCTGAAGGAGAGGAGAGAGGAAAATGGATACAATA
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 TKKENCPYSI LEITSVEIGV
VAVKAINSNY YLAMNKKGKL YGSKEFNNDC KLKERREENG YNTYASFNWQ HNGRQMYVAL
NGKGAPRRGQ KTRRKNTSAH FLPMVVHS*
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
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