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: ENST00000271651
MT speed 0 s - this script 3.131478 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CTSK	disease_causing	0.999999998813679	simple_aae				L309P	single base exchange	rs29001685		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999998813679 (explain)

Summary

amino acid sequence changed
known as potential disease variant: rs8426 (probable pathogenic)
known disease mutation at this position (HGMD CM001110)
protein features (might be) affected

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:150769339A>GN/A show variant in all transcripts IGV

HGNC symbol

CTSK

Ensembl transcript ID

ENST00000271651

Genbank transcript ID

NM_000396

UniProt peptide

P43235

alteration type

single base exchange

alteration region

CDS

DNA changes

c.926T>C
cDNA.1037T>C
g.11461T>C

AA changes

L309P Score: 98 explain score(s)

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

309

frameshift

known variant

Reference ID: rs29001685
Allele 'G' was neither found in ExAC nor 1000G.
known as potential disease variant: rs8426 (probable pathogenic for Pyknodysostosis) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM001110)

known disease mutation at this position, please check HGMD for details (HGMD ID CM001110)
known disease mutation at this position, please check HGMD for details (HGMD ID CM001110)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	0.039	0.987
	0.756	0.993
(flanking)	1.118	0.998

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

splice sites

no abrogation of potential splice sites

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

309

mutated

not conserved

309

Ptroglodytes

all identical

ENSPTRG00000001265

309

Mmulatta

all identical

ENSMMUG00000000537

309

Fcatus

all identical

ENSFCAG00000003643

310

Mmusculus

all identical

ENSMUSG00000028111

309

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000000525

316

Drerio

all identical

ENSDARG00000040251

312

Dmelanogaster

not conserved

FBgn0013770

351

Celegans

not conserved

T03E6.7

316

Xtropicalis

all identical

ENSXETG00000008929

314

protein features

start (aa)	end (aa)	feature	details
307	316	STRAND		lost

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

990 / 990

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

330 / 330

position of stopcodon in wt / mu cDNA

1101 / 1101

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

112 / 112

chromosome

strand

-1

last intron/exon boundary

1002

theoretical NMD boundary in CDS

840

length of CDS

990

coding sequence (CDS) position

926

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

1037

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

11461

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

150769339

original gDNA sequence snippet

GGGAAACAAAGGATATATCCTCATGGCTCGAAATAAGAACA

altered gDNA sequence snippet

GGGAAACAAAGGATATATCCCCATGGCTCGAAATAAGAACA

original cDNA sequence snippet

GGGAAACAAAGGATATATCCTCATGGCTCGAAATAAGAACA

altered cDNA sequence snippet

GGGAAACAAAGGATATATCCCCATGGCTCGAAATAAGAACA

wildtype AA sequence

MWGLKVLLLP VVSFALYPEE ILDTHWELWK KTHRKQYNNK VDEISRRLIW EKNLKYISIH
NLEASLGVHT YELAMNHLGD MTSEEVVQKM TGLKVPLSHS RSNDTLYIPE WEGRAPDSVD
YRKKGYVTPV KNQGQCGSCW AFSSVGALEG QLKKKTGKLL NLSPQNLVDC VSENDGCGGG
YMTNAFQYVQ KNRGIDSEDA YPYVGQEESC MYNPTGKAAK CRGYREIPEG NEKALKRAVA
RVGPVSVAID ASLTSFQFYS KGVYYDESCN SDNLNHAVLA VGYGIQKGNK HWIIKNSWGE
NWGNKGYILM ARNKNNACGI ANLASFPKM*

mutated AA sequence

speed

1.12 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