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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 2.503507 s

Results


genesymbolpredictionprobabilitymodelprediction
problem
splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
FGF23disease_causing_automatic0.804587976883923simple_aaeaffected0R176Qsingle base exchangers104894347show file

Taster files

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documentation

Prediction

disease causing

Model: simple_aae, prob: 0.804587976883923 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM002776)
  • known disease mutation: rs5025 (pathogenic)
  • protein features (might be) affected
  • splice site changes
hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:4479738C>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.527G>A
cDNA.673G>A
g.9157G>A
AA changes R176Q Score: 43 explain score(s)
position(s) of altered AA
if AA alteration in CDS
176
frameshift no
known variant Reference ID: rs104894347
Allele 'T' was neither found in ExAC nor 1000G.
known disease mutation: rs5025 (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 CM002776)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002776)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002776)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-1.190.501
3.5880.902
(flanking)0.6550.901
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Donor gained91520.48mu: ATACCACGGCAGCAC ACCA|cggc
distance from splice site 212
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      176PLIHFNTPIPRRHTRSAEDDSERD
mutated  all conserved    176PLIHFNTPIPRQHTRS
Ptroglodytes  all identical  ENSPTRG00000004551  176PLIHFNTPIPRRHTRS
Mmulatta  all identical  ENSMMUG00000014978  176PLIHFNTPRPRRHTRS
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000000182  176PLLHFYTVRPRRHTRS
Ggallus  all identical  ENSGALG00000017286  179PLFRFNTPEPHRNTRSADVD-PL
Trubripes  not conserved  ENSTRUG00000011062  48PLVGSNWGNPRRYIHLQTSTDISNF
Drerio  not conserved  ENSDARG00000045854  186PLERL-----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.might get lost (downstream of altered splice site)
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 527
cDNA position
(for ins/del: last normal base / first normal base)
673
gDNA position
(for ins/del: last normal base / first normal base)
9157
chromosomal position
(for ins/del: last normal base / first normal base)
4479738
original gDNA sequence snippet CAACACCCCCATACCACGGCGGCACACCCGGAGCGCCGAGG
altered gDNA sequence snippet CAACACCCCCATACCACGGCAGCACACCCGGAGCGCCGAGG
original cDNA sequence snippet CAACACCCCCATACCACGGCGGCACACCCGGAGCGCCGAGG
altered cDNA sequence snippet CAACACCCCCATACCACGGCAGCACACCCGGAGCGCCGAGG
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 TPIPRQHTRS
AEDDSERDPL NVLKPRARMT PAPASCSQEL PSAEDNSPMA SDPLGVVRGG RVNTHAGGTG
PEGCRPFAKF I*
speed 0.35 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