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 2.371196 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CTSK	disease_causing_automatic	0.999999999998726	simple_aae		affected	0	G146R	single base exchange	rs74315302		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999998726 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM960425)
known disease mutation: rs8421 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr1:150776679C>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.436G>C
cDNA.547G>C
g.4121G>C

AA changes

G146R Score: 125 explain score(s)

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

146

frameshift

known variant

Reference ID: rs74315302
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs8421 (pathogenic for Pyknodysostosis|Inborn genetic diseases|not provided) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960425)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960425)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960425)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	5.582	1
	5.582	1
(flanking)	0.675	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 marginally increased	4116	wt: 0.5809 / mu: 0.5906 (marginal change - not scored)	wt: TTCCTGTTGGGCTTTTAGCTCTGTGGGTGCCCTGGAGGGCC mu: TTCCTGTTGGGCTTTTAGCTCTGTGCGTGCCCTGGAGGGCC	gctc\|TGTG
Acc marginally increased	4112	wt: 0.7301 / mu: 0.7975 (marginal change - not scored)	wt: GTGGTTCCTGTTGGGCTTTTAGCTCTGTGGGTGCCCTGGAG mu: GTGGTTCCTGTTGGGCTTTTAGCTCTGTGCGTGCCCTGGAG	ttta\|GCTC
Acc increased	4118	wt: 0.26 / mu: 0.44	wt: CCTGTTGGGCTTTTAGCTCTGTGGGTGCCCTGGAGGGCCAA mu: CCTGTTGGGCTTTTAGCTCTGTGCGTGCCCTGGAGGGCCAA	tctg\|TGGG
Acc marginally increased	4121	wt: 0.9601 / mu: 0.9673 (marginal change - not scored)	wt: GTTGGGCTTTTAGCTCTGTGGGTGCCCTGGAGGGCCAACTC mu: GTTGGGCTTTTAGCTCTGTGCGTGCCCTGGAGGGCCAACTC	gtgg\|GTGC
Donor increased	4112	wt: 0.23 / mu: 0.44	wt: CTTTTAGCTCTGTGG mu: CTTTTAGCTCTGTGC	TTTA\|gctc
Donor increased	4126	wt: 0.61 / mu: 0.82	wt: GGTGCCCTGGAGGGC mu: CGTGCCCTGGAGGGC	TGCC\|ctgg
Acc gained	4123	0.84	mu: TGGGCTTTTAGCTCTGTGCGTGCCCTGGAGGGCCAACTCAA	gcgt\|GCCC
Acc gained	4128	0.51	mu: TTTTAGCTCTGTGCGTGCCCTGGAGGGCCAACTCAAGAAGA	ccct\|GGAG

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

146

mutated

not conserved

146

Ptroglodytes

all identical

ENSPTRG00000001265

146

Mmulatta

all identical

ENSMMUG00000000537

146

Fcatus

all identical

ENSFCAG00000003643

147

Mmusculus

all identical

ENSMUSG00000028111

146

Ggallus

no homologue

Trubripes

all identical

ENSTRUG00000000525

152

Drerio

all identical

ENSDARG00000040251

149

Dmelanogaster

all identical

FBgn0013770

185

Celegans

all identical

T03E6.7

151

Xtropicalis

all identical

ENSXETG00000008929

153

protein features

start (aa)	end (aa)	feature	details
139	156	HELIX		lost
164	170	HELIX		might get lost (downstream of altered splice site)
170	170	DISULFID		might get lost (downstream of altered splice site)
176	178	HELIX		might get lost (downstream of altered splice site)
177	177	DISULFID		might get lost (downstream of altered splice site)
182	192	HELIX		might get lost (downstream of altered splice site)
195	197	STRAND		might get lost (downstream of altered splice site)
198	200	TURN		might get lost (downstream of altered splice site)
210	210	DISULFID		might get lost (downstream of altered splice site)
214	216	HELIX		might get lost (downstream of altered splice site)
217	219	STRAND		might get lost (downstream of altered splice site)
224	226	STRAND		might get lost (downstream of altered splice site)
232	241	HELIX		might get lost (downstream of altered splice site)
245	249	STRAND		might get lost (downstream of altered splice site)
254	257	HELIX		might get lost (downstream of altered splice site)
261	264	STRAND		might get lost (downstream of altered splice site)
269	269	DISULFID		might get lost (downstream of altered splice site)
276	276	ACT_SITE	By similarity.	might get lost (downstream of altered splice site)
276	286	STRAND		might get lost (downstream of altered splice site)
289	295	STRAND		might get lost (downstream of altered splice site)
296	296	ACT_SITE	By similarity.	might get lost (downstream of altered splice site)
300	302	STRAND		might get lost (downstream of altered splice site)
303	305	TURN		might get lost (downstream of altered splice site)
307	316	STRAND		might get lost (downstream of altered splice site)
317	319	HELIX		might get lost (downstream of altered splice site)
318	318	DISULFID		might get lost (downstream of altered splice site)
320	322	TURN		might get lost (downstream of altered splice site)
325	327	STRAND		might get lost (downstream of altered splice site)

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

436

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

547

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

4121

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

150776679

original gDNA sequence snippet

GTTGGGCTTTTAGCTCTGTGGGTGCCCTGGAGGGCCAACTC

altered gDNA sequence snippet

GTTGGGCTTTTAGCTCTGTGCGTGCCCTGGAGGGCCAACTC

original cDNA sequence snippet

GTTGGGCTTTTAGCTCTGTGGGTGCCCTGGAGGGCCAACTC

altered cDNA sequence snippet

GTTGGGCTTTTAGCTCTGTGCGTGCCCTGGAGGGCCAACTC

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

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

speed

0.30 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