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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 1 s - this script 3.171492 s

Results

genesymbolpredictionprobabilitymodelprediction
problem		splicingClinVaramino acid changesvariant typedbSNP IDprotein lengthfile
FGF23disease_causing_automatic1simple_aaeaffected0S71Gsingle base exchangers104894342show file

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Prediction

disease causing

 Model: simple_aae, prob: 1 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM050257)
  • known disease mutation: rs5027 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr12:4488538T>CN/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.211A>G
cDNA.357A>G
g.357A>G
AA changes S71G Score: 56 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 71
frameshift no
known variant Reference ID: rs104894342
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC022

known disease mutation: rs5027 (pathogenic for Tumoral calcinosis, hyperphosphatemic, familial|Tumoral calcinosis, hyperphosphatemic, familial, 2|Hyperphosphatemic familial tumoral calcinosis 1|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM050257)

known disease mutation at this position, please check HGMD for details (HGMD ID CM050257)
known disease mutation at this position, please check HGMD for details (HGMD ID CM050257)
regulatory features Promoter Associated, Regulatory Feature, Promoter like regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
DNase1, Open Chromatin, DNase1 Hypersensitive Site
phyloP / phastCons
PhyloPPhastCons
(flanking)3.8091
3.1751
(flanking)1.5381
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites alteration within used splice site, likely to disturb normal splicing
effectgDNA positionscoredetection sequence  exon-intron border
Donor lost357sequence motif lost- wt: TACA|gtga
 mu: TACG.gtga
Acc marginally increased361wt: 0.2943 / mu: 0.3284 (marginal change - not scored)wt: CCATCAGACCATCTACAGTGAGTAGGGCTTCAGGCTGGGAA
mu: CCATCAGACCATCTACGGTGAGTAGGGCTTCAGGCTGGGAA		 gtga|GTAG
Donor increased356wt: 0.85 / mu: 0.98wt: ATCTACAGTGAGTAG
mu: ATCTACGGTGAGTAG		 CTAC|agtg
Donor decreased357wt: 0.84 / mu: 0.26wt: TCTACAGTGAGTAGG
mu: TCTACGGTGAGTAGG		 TACA|gtga
Donor gained3510.66mu: AGACCATCTACGGTG ACCA|tcta
distance from splice site 2
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      71HVDGAPHQTIYSALMIRSEDAGFV
mutated  not conserved    71VDGAPHQTIYGALMIRSEDAGF
Ptroglodytes  all identical  ENSPTRG00000004551  71VDGAPHQTIYSALMIRSEDAGF
Mmulatta  all identical  ENSMMUG00000014978  71VDGAPHQTIYSALMIRSEDAGF
Fcatus  no homologue    
Mmusculus  all identical  ENSMUSG00000000182  71VDGTPHQTIYSALMITSEDAGS
Ggallus  all identical  ENSGALG00000017286  74SALMIKSEGAGC
Trubripes  all identical  ENSTRUG00000011062  78TVRKSTARTSYSVILLKAETRER
Drerio  all identical  ENSDARG00000045854  81KTTNRGSYSVILLKTESRDR
Dmelanogaster  no homologue    
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
6971TURNlost
7377STRANDmight get lost (downstream of altered splice site)
7981HELIXmight get lost (downstream of altered splice site)
8287STRANDmight get lost (downstream of altered splice site)
8891TURNmight get lost (downstream of altered splice site)
9296STRANDmight get lost (downstream of altered splice site)
9595DISULFIDmight get lost (downstream of altered splice site)
102107STRANDmight get lost (downstream of altered splice site)
110112TURNmight get lost (downstream of altered splice site)
113113DISULFIDmight get lost (downstream of altered splice site)
115119STRANDmight get lost (downstream of altered splice site)
125128STRANDmight get lost (downstream of altered splice site)
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 211
cDNA position
(for ins/del: last normal base / first normal base)		 357
gDNA position
(for ins/del: last normal base / first normal base)		 357
chromosomal position
(for ins/del: last normal base / first normal base)		 4488538
original gDNA sequence snippet CACCCCATCAGACCATCTACAGTGAGTAGGGCTTCAGGCTG
altered gDNA sequence snippet CACCCCATCAGACCATCTACGGTGAGTAGGGCTTCAGGCTG
original cDNA sequence snippet CACCCCATCAGACCATCTACAGTGCCCTGATGATCAGATCA
altered cDNA sequence snippet CACCCCATCAGACCATCTACGGTGCCCTGATGATCAGATCA
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 GALMIRSEDA GFVVITGVMS RRYLCMDFRG NIFGSHYFDP ENCRFQHQTL
ENGYDVYHSP QYHFLVSLGR AKRAFLPGMN PPPYSQFLSR RNEIPLIHFN TPIPRRHTRS
AEDDSERDPL NVLKPRARMT PAPASCSQEL PSAEDNSPMA SDPLGVVRGG RVNTHAGGTG
PEGCRPFAKF I*
speed 1.00 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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