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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 2.305042 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
FGF23disease_causing_automatic0.999999876300025simple_aaeaffected0R179Qsingle base exchangers193922702show file

Taster files

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 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999999876300025 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM002777)
  • known disease mutation: rs36135 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:4479729C>TN/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.536G>A
cDNA.682G>A
g.9166G>A
AA changes R179Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 179
frameshift no
known variant Reference ID: rs193922702
databasehomozygous (T/T)heterozygousallele carriers
1000G---
ExAC011

known disease mutation: rs36135 (pathogenic for Autosomal dominant hypophosphatemic rickets|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM002777)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002777)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002777)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-0.5290.917
4.010.988
(flanking)2.2440.981
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor increased9168wt: 0.50 / mu: 0.69wt: CCCGGAGCGCCGAGG
mu: CCCAGAGCGCCGAGG		 CGGA|gcgc
Donor increased9163wt: 0.72 / mu: 0.82wt: GCACACCCGGAGCGC
mu: GCACACCCAGAGCGC		 ACAC|ccgg
Donor marginally increased9170wt: 0.9713 / mu: 0.9899 (marginal change - not scored)wt: CGGAGCGCCGAGGAC
mu: CAGAGCGCCGAGGAC		 GAGC|gccg
distance from splice site 221
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      179HFNTPIPRRHTRSAEDDSERDPLN
mutated  all conserved    179HFNTPIPRRHTQSAEDDSERDPL
Ptroglodytes  all identical  ENSPTRG00000004551  179HFNTPIPRRHTRSAEDDSERDPL
Mmulatta  all identical  ENSMMUG00000014978  179HFNTPRPRRHTRSAEDDSERDPL
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000000182  179HFYTVRPRRHTRSAEDPPERDPL
Ggallus  all identical  ENSGALG00000017286  182RFNTPEPHRNTRSADVD-PLDPH
Trubripes  all conserved  ENSTRUG00000011062  51GSNWGNPRRYIHLQTSTDISNFYLE
Drerio  all identical  ENSDARG00000045854  189RL-----QHRERRNR
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
178178CARBOHYDO-linked (GalNAc).might get lost (downstream of altered splice site)
179180SITECleavage; by proprotein convertases.lost
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 536
cDNA position
(for ins/del: last normal base / first normal base)		 682
gDNA position
(for ins/del: last normal base / first normal base)		 9166
chromosomal position
(for ins/del: last normal base / first normal base)		 4479729
original gDNA sequence snippet CATACCACGGCGGCACACCCGGAGCGCCGAGGACGACTCGG
altered gDNA sequence snippet CATACCACGGCGGCACACCCAGAGCGCCGAGGACGACTCGG
original cDNA sequence snippet CATACCACGGCGGCACACCCGGAGCGCCGAGGACGACTCGG
altered cDNA sequence snippet CATACCACGGCGGCACACCCAGAGCGCCGAGGACGACTCGG
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 RRYLCMDFRG NIFGSHYFDP ENCRFQHQTL
ENGYDVYHSP QYHFLVSLGR AKRAFLPGMN PPPYSQFLSR RNEIPLIHFN TPIPRRHTQS
AEDDSERDPL NVLKPRARMT PAPASCSQEL PSAEDNSPMA SDPLGVVRGG RVNTHAGGTG
PEGCRPFAKF I*
speed 0.25 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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