Yum, tasty mutations...

MutationTaster - study a chromosomal position

 MTQE documentation
NEVER press reload or F5 - unless you want to start from the very beginning.
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 0.78 s - this script 2.975323 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
FGF23disease_causing_automatic0.986622206185587simple_aaeaffected0S129Fsingle base exchangers104894344show file

Taster files

Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.986622206185587 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM053891)
  • known disease mutation: rs5029 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:4479879G>AN/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.386C>T
cDNA.532C>T
g.9016C>T
AA changes S129F Score: 155 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 129
frameshift no
known variant Reference ID: rs104894344
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs5029 (pathogenic for Tumoral calcinosis, hyperphosphatemic, familial, 2) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM053891)

known disease mutation at this position, please check HGMD for details (HGMD ID CM053891)
known disease mutation at this position, please check HGMD for details (HGMD ID CM053891)
regulatory features H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
phyloP / phastCons
PhyloPPhastCons
(flanking)-2.2230.256
1.6740.603
(flanking)1.9530.626
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc increased9026wt: 0.60 / mu: 0.66wt: GTCTACCACTCTCCTCAGTATCACTTCCTGGTCAGTCTGGG
mu: GTCTACCACTTTCCTCAGTATCACTTCCTGGTCAGTCTGGG		 gtat|CACT
Acc marginally increased9022wt: 0.9751 / mu: 0.9804 (marginal change - not scored)wt: CGACGTCTACCACTCTCCTCAGTATCACTTCCTGGTCAGTC
mu: CGACGTCTACCACTTTCCTCAGTATCACTTCCTGGTCAGTC		 ctca|GTAT
Acc increased9021wt: 0.33 / mu: 0.44wt: ACGACGTCTACCACTCTCCTCAGTATCACTTCCTGGTCAGT
mu: ACGACGTCTACCACTTTCCTCAGTATCACTTCCTGGTCAGT		 cctc|AGTA
distance from splice site 71
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      129QTLENGYDVYHSPQYHFLVSLGRA
mutated  not conserved    129ENGYDVYHFPQYHFLVSLGR
Ptroglodytes  all identical  ENSPTRG00000004551  129ENGYDVYYSPQYHFLVSLGR
Mmulatta  all identical  ENSMMUG00000014978  129ENGYDVYHSPQHHFLVSLGR
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000000182  129ENGYDVYLSQKHHYLVSLGR
Ggallus  all identical  ENSGALG00000017286  132RTLENGYDVYQSPKHNFLVSLGR
Trubripes  all identical  ENSTRUG00000011062  139SLLENNRDVYYSSRTGILFNLEG
Drerio  all identical  ENSDARG00000045854  139HRDVYYSTKHSILLNLDG
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
130132TURNmight get lost (downstream of altered splice site)
138140STRANDmight get lost (downstream of altered splice site)
153155HELIXmight get lost (downstream of altered splice site)
157161STRANDmight get lost (downstream of altered splice site)
166168HELIXmight get lost (downstream of altered splice site)
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 386
cDNA position
(for ins/del: last normal base / first normal base)		 532
gDNA position
(for ins/del: last normal base / first normal base)		 9016
chromosomal position
(for ins/del: last normal base / first normal base)		 4479879
original gDNA sequence snippet CGGGTACGACGTCTACCACTCTCCTCAGTATCACTTCCTGG
altered gDNA sequence snippet CGGGTACGACGTCTACCACTTTCCTCAGTATCACTTCCTGG
original cDNA sequence snippet CGGGTACGACGTCTACCACTCTCCTCAGTATCACTTCCTGG
altered cDNA sequence snippet CGGGTACGACGTCTACCACTTTCCTCAGTATCACTTCCTGG
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
ENGYDVYHFP QYHFLVSLGR AKRAFLPGMN PPPYSQFLSR RNEIPLIHFN TPIPRRHTRS
AEDDSERDPL NVLKPRARMT PAPASCSQEL PSAEDNSPMA SDPLGVVRGG RVNTHAGGTG
PEGCRPFAKF I*
speed 0.78 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
back to results table

Problems