MutationTaster - study a chromosomal position

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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 2.738043 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
FGF23	disease_causing_automatic	0.999999937632402	simple_aae			0	R179W	single base exchange	rs28937882		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999937632402 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM002778)
known disease mutation: rs5026 (pathogenic)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr12:4479730G>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.535C>T
cDNA.681C>T
g.9165C>T

AA changes

R179W Score: 101 explain score(s)

position(s) of altered AA
if AA alteration in CDS

179

frameshift

known variant

Reference ID: rs28937882
Allele 'A' was neither found in ExAC nor 1000G.
known disease mutation: rs5026 (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 CM002778)

known disease mutation at this position, please check HGMD for details (HGMD ID CM002778)
known disease mutation at this position, please check HGMD for details (HGMD ID CM002778)

regulatory features

H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.01	0.988
	2.244	0.981
(flanking)	-1.019	0.776

explain score(s) and/or inspect your position(s) in in UCSC Genome Browser

splice sites

effect	gDNA position	score	wt detection sequence	exon-intron border
Donor marginally increased	9168	wt: 0.4961 / mu: 0.5118 (marginal change - not scored)	wt: CCCGGAGCGCCGAGG mu: CCTGGAGCGCCGAGG	CGGA\|gcgc
Donor marginally increased	9163	wt: 0.7220 / mu: 0.7340 (marginal change - not scored)	wt: GCACACCCGGAGCGC mu: GCACACCTGGAGCGC	ACAC\|ccgg

distance from splice site

220

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

179

mutated

not conserved

179

Ptroglodytes

all identical

ENSPTRG00000004551

179

Mmulatta

all identical

ENSMMUG00000014978

179

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000000182

179

Ggallus

all identical

ENSGALG00000017286

182

Trubripes

all conserved

ENSTRUG00000011062

RYI

Drerio

all identical

ENSDARG00000045854

189

Dmelanogaster

no homologue

Celegans

no homologue

Xtropicalis

no homologue

protein features

start (aa)	end (aa)	feature	details
179	180	SITE	Cleavage; 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

strand

-1

last intron/exon boundary

462

theoretical NMD boundary in CDS

265

length of CDS

756

coding sequence (CDS) position

535

cDNA position
(for ins/del: last normal base / first normal base)

681

gDNA position
(for ins/del: last normal base / first normal base)

9165

chromosomal position
(for ins/del: last normal base / first normal base)

4479730

original gDNA sequence snippet

CCATACCACGGCGGCACACCCGGAGCGCCGAGGACGACTCG

altered gDNA sequence snippet

CCATACCACGGCGGCACACCTGGAGCGCCGAGGACGACTCG

original cDNA sequence snippet

CCATACCACGGCGGCACACCCGGAGCGCCGAGGACGACTCG

altered cDNA sequence snippet

CCATACCACGGCGGCACACCTGGAGCGCCGAGGACGACTCG

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 TPIPRRHTWS
AEDDSERDPL NVLKPRARMT PAPASCSQEL PSAEDNSPMA SDPLGVVRGG RVNTHAGGTG
PEGCRPFAKF I*

speed

0.73 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

MutationTaster - study a chromosomal position

Results

Taster files

mutation t@sting

Prediction

disease causing

Problems