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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: ENST00000237837
MT speed 0 s - this script 2.82738 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
FGF23disease_causing_automatic0.999993151668765simple_aae0M96Tsingle base exchangers104894343show file

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Prediction

disease causing

 Model: simple_aae, prob: 0.999993151668765 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM054726)
  • known disease mutation: rs5028 (pathogenic)
  • protein features (might be) affected
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:4481788A>GN/A show variant in all transcripts   IGV
HGNC symbol FGF23
Ensembl transcript ID ENST00000237837
Genbank transcript ID NM_020638
UniProt peptide Q9GZV9
alteration type single base exchange
alteration region CDS
DNA changes c.287T>C
cDNA.433T>C
g.7107T>C
AA changes M96T Score: 81 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 96
frameshift no
known variant Reference ID: rs104894343
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs5028 (pathogenic for Tumoral calcinosis, hyperphosphatemic, familial, 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM054726)

known disease mutation at this position, please check HGMD for details (HGMD ID CM054726)
known disease mutation at this position, please check HGMD for details (HGMD ID CM054726)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)3.9141
3.2681
(flanking)3.2681
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites no abrogation of potential splice sites
distance from splice site 29
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      96ITGVMSRRYLCMDFRGNIFGSHYF
mutated  not conserved    96ITGVMSRRYLCTDFRGNIFGSHY
Ptroglodytes  all identical  ENSPTRG00000004551  96ITGVMSRRYLCMDFRGNIFGSHY
Mmulatta  all identical  ENSMMUG00000014978  96ITGVMSRRYLCMDFRGNIFGSHY
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000000182  96ITGAMTRRFLCMDLHGNIFGSLH
Ggallus  all identical  ENSGALG00000017286  99ITGVKSGRYLCMDMKGDIFGSYY
Trubripes  all identical  ENSTRUG00000011062  106ILGVKSNRYLCMDLEGKPFSSPT
Drerio  all identical  ENSDARG00000045854  106IFGVKSNRFLCMDTGGTLFTSTI
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
9296STRANDlost
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 756 / 756
position (AA) of stopcodon in wt / mu AA sequence 252 / 252
position of stopcodon in wt / mu cDNA 902 / 902
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 147 / 147
chromosome 12
strand -1
last intron/exon boundary 462
theoretical NMD boundary in CDS 265
length of CDS 756
coding sequence (CDS) position 287
cDNA position
(for ins/del: last normal base / first normal base)		 433
gDNA position
(for ins/del: last normal base / first normal base)		 7107
chromosomal position
(for ins/del: last normal base / first normal base)		 4481788
original gDNA sequence snippet GAGCAGAAGATACCTCTGCATGGATTTCAGAGGCAACATTT
altered gDNA sequence snippet GAGCAGAAGATACCTCTGCACGGATTTCAGAGGCAACATTT
original cDNA sequence snippet GAGCAGAAGATACCTCTGCATGGATTTCAGAGGCAACATTT
altered cDNA sequence snippet GAGCAGAAGATACCTCTGCACGGATTTCAGAGGCAACATTT
wildtype AA sequence MLGARLRLWV CALCSVCSMS VLRAYPNASP LLGSSWGGLI HLYTATARNS YHLQIHKNGH
VDGAPHQTIY SALMIRSEDA GFVVITGVMS RRYLCMDFRG NIFGSHYFDP ENCRFQHQTL
ENGYDVYHSP QYHFLVSLGR AKRAFLPGMN PPPYSQFLSR RNEIPLIHFN TPIPRRHTRS
AEDDSERDPL NVLKPRARMT PAPASCSQEL PSAEDNSPMA SDPLGVVRGG RVNTHAGGTG
PEGCRPFAKF I*
mutated AA sequence MLGARLRLWV CALCSVCSMS VLRAYPNASP LLGSSWGGLI HLYTATARNS YHLQIHKNGH
VDGAPHQTIY SALMIRSEDA GFVVITGVMS RRYLCTDFRG NIFGSHYFDP ENCRFQHQTL
ENGYDVYHSP QYHFLVSLGR AKRAFLPGMN PPPYSQFLSR RNEIPLIHFN TPIPRRHTRS
AEDDSERDPL NVLKPRARMT PAPASCSQEL PSAEDNSPMA SDPLGVVRGG RVNTHAGGTG
PEGCRPFAKF I*
speed 0.77 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