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: ENST00000373115
MT speed 0 s - this script 2.820308 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CHST3	disease_causing_automatic	0.999999999949064	simple_aae		affected	0	L307P	single base exchange	rs121908618		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999949064 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM082557)
known disease mutation: rs6044 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr10:73767709T>CN/A show variant in all transcripts IGV

HGNC symbol

CHST3

Ensembl transcript ID

ENST00000373115

Genbank transcript ID

NM_004273

UniProt peptide

Q7LGC8

alteration type

single base exchange

alteration region

CDS

DNA changes

c.920T>C
cDNA.1357T>C
g.43587T>C

AA changes

L307P Score: 98 explain score(s)

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

307

frameshift

known variant

Reference ID: rs121908618
Allele 'C' was neither found in ExAC nor 1000G.
known disease mutation: rs6044 (pathogenic for Spondyloepiphyseal dysplasia with congenital joint dislocations) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM082557)

known disease mutation at this position, please check HGMD for details (HGMD ID CM082557)
known disease mutation at this position, please check HGMD for details (HGMD ID CM082557)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	3.2	1
	2.293	1
(flanking)	1.724	1

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
Acc increased	43588	wt: 0.24 / mu: 0.29	wt: CGCGACCCCCGGGCCGTGCTGGCCTCGCGCATGGTGGCCTT mu: CGCGACCCCCGGGCCGTGCCGGCCTCGCGCATGGTGGCCTT	gctg\|GCCT

distance from splice site

780

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

307

mutated

not conserved

307

Ptroglodytes

all identical

ENSPTRG00000002607

307

Mmulatta

all identical

ENSMMUG00000014783

312

Fcatus

no homologue

Mmusculus

all identical

ENSMUSG00000057337

307

Ggallus

all identical

ENSGALG00000024056

279

Trubripes

all identical

ENSTRUG00000011960

267

Drerio

no homologue

Dmelanogaster

all conserved

FBgn0051637

332

Celegans

no homologue

Xtropicalis

all identical

ENSXETG00000032713

291

protein features

start (aa)	end (aa)	feature	details
39	479	TOPO_DOM	Lumenal (Potential).	lost
301	309	NP_BIND	PAPS (By similarity).	lost
387	387	CONFLICT	R -> P (in Ref. 1; BAA32576).	might get lost (downstream of altered splice site)
420	420	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)
443	443	CONFLICT	A -> P (in Ref. 1; BAA32576).	might get lost (downstream of altered splice site)
464	464	CARBOHYD	N-linked (GlcNAc...) (Potential).	might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1440 / 1440

position (AA) of stopcodon in wt / mu AA sequence

480 / 480

position of stopcodon in wt / mu cDNA

1877 / 1877

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

438 / 438

chromosome

strand

last intron/exon boundary

578

theoretical NMD boundary in CDS

length of CDS

1440

coding sequence (CDS) position

920

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

1357

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

43587

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

73767709

original gDNA sequence snippet

GCGCGACCCCCGGGCCGTGCTGGCCTCGCGCATGGTGGCCT

altered gDNA sequence snippet

GCGCGACCCCCGGGCCGTGCCGGCCTCGCGCATGGTGGCCT

original cDNA sequence snippet

GCGCGACCCCCGGGCCGTGCTGGCCTCGCGCATGGTGGCCT

altered cDNA sequence snippet

GCGCGACCCCCGGGCCGTGCCGGCCTCGCGCATGGTGGCCT

wildtype AA sequence

MEKGLTLPQD CRDFVHSLKM RSKYALFLVF VVIVFVFIEK ENKIISRVSD KLKQIPQALA
DANSTDPALI LAENASLLSL SELDSAFSQL QSRLRNLSLQ LGVEPAMEAA GEEEEEQRKE
EEPPRPAVAG PRRHVLLMAT TRTGSSFVGE FFNQQGNIFY LFEPLWHIER TVSFEPGGAN
AAGSALVYRD VLKQLFLCDL YVLEHFITPL PEDHLTQFMF RRGSSRSLCE DPVCTPFVKK
VFEKYHCKNR RCGPLNVTLA AEACRRKEHM ALKAVRIRQL EFLQPLAEDP RLDLRVIQLV
RDPRAVLASR MVAFAGKYKT WKKWLDDEGQ DGLREEEVQR LRGNCESIRL SAELGLRQPA
WLRGRYMLVR YEDVARGPLQ KAREMYRFAG IPLTPQVEDW IQKNTQAAHD GSGIYSTQKN
SSEQFEKWRF SMPFKLAQVV QAACGPAMRL FGYKLARDAA ALTNRSVSLL EERGTFWVT*

mutated AA sequence

MEKGLTLPQD CRDFVHSLKM RSKYALFLVF VVIVFVFIEK ENKIISRVSD KLKQIPQALA
DANSTDPALI LAENASLLSL SELDSAFSQL QSRLRNLSLQ LGVEPAMEAA GEEEEEQRKE
EEPPRPAVAG PRRHVLLMAT TRTGSSFVGE FFNQQGNIFY LFEPLWHIER TVSFEPGGAN
AAGSALVYRD VLKQLFLCDL YVLEHFITPL PEDHLTQFMF RRGSSRSLCE DPVCTPFVKK
VFEKYHCKNR RCGPLNVTLA AEACRRKEHM ALKAVRIRQL EFLQPLAEDP RLDLRVIQLV
RDPRAVPASR MVAFAGKYKT WKKWLDDEGQ DGLREEEVQR LRGNCESIRL SAELGLRQPA
WLRGRYMLVR YEDVARGPLQ KAREMYRFAG IPLTPQVEDW IQKNTQAAHD GSGIYSTQKN
SSEQFEKWRF SMPFKLAQVV QAACGPAMRL FGYKLARDAA ALTNRSVSLL EERGTFWVT*

speed

0.81 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