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: ENST00000227266
MT speed 0 s - this script 3.026984 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CTSC	disease_causing_automatic	1	simple_aae			0	W429C	single base exchange	rs104894215		show file

Taster files

mutation t@sting

documentation

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 CM013701)
known disease mutation: rs7298 (pathogenic)

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:88027279C>GN/A show variant in all transcripts IGV

HGNC symbol

CTSC

Ensembl transcript ID

ENST00000227266

Genbank transcript ID

NM_001814

UniProt peptide

P53634

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1287G>C
cDNA.1402G>C
g.43677G>C

AA changes

W429C Score: 215 explain score(s)

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

429

frameshift

known variant

Reference ID: rs104894215
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs7298 (pathogenic for Papillon-Lefèvre syndrome) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM013701)

known disease mutation at this position, please check HGMD for details (HGMD ID CM013701)
known disease mutation at this position, please check HGMD for details (HGMD ID CM013701)

regulatory features

DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	4.668	1
	6.323	1
(flanking)	6.323	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
Donor marginally increased	43672	wt: 0.9125 / mu: 0.9785 (marginal change - not scored)	wt: AAAACAGCTGGGGCA mu: AAAACAGCTGCGGCA	AACA\|gctg

distance from splice site

398

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

429

mutated

not conserved

429

Ptroglodytes

all identical

ENSPTRG00000004152

429

Mmulatta

all identical

ENSMMUG00000022139

429

Fcatus

all identical

ENSFCAG00000008445

429

Mmusculus

all identical

ENSMUSG00000030560

428

Ggallus

all identical

ENSGALG00000017239

429

Trubripes

all identical

ENSTRUG00000006734

428

Drerio

all identical

ENSDARG00000018806

421

Dmelanogaster

no homologue

Celegans

all identical

F15D4.4

427

Xtropicalis

all identical

ENSXETG00000011748

424

protein features

no protein features affected

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1392 / 1392

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

464 / 464

position of stopcodon in wt / mu cDNA

1507 / 1507

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

116 / 116

chromosome

strand

-1

last intron/exon boundary

1005

theoretical NMD boundary in CDS

839

length of CDS

1392

coding sequence (CDS) position

1287

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

1402

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

43677

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

88027279

original gDNA sequence snippet

TGGATTGTTAAAAACAGCTGGGGCACCGGCTGGGGTGAGAA

altered gDNA sequence snippet

TGGATTGTTAAAAACAGCTGCGGCACCGGCTGGGGTGAGAA

original cDNA sequence snippet

TGGATTGTTAAAAACAGCTGGGGCACCGGCTGGGGTGAGAA

altered cDNA sequence snippet

TGGATTGTTAAAAACAGCTGCGGCACCGGCTGGGGTGAGAA

wildtype AA sequence

MGAGPSLLLA ALLLLLSGDG AVRCDTPANC TYLDLLGTWV FQVGSSGSQR DVNCSVMGPQ
EKKVVVYLQK LDTAYDDLGN SGHFTIIYNQ GFEIVLNDYK WFAFFKYKEE GSKVTTYCNE
TMTGWVHDVL GRNWACFTGK KVGTASENVY VNIAHLKNSQ EKYSNRLYKY DHNFVKAINA
IQKSWTATTY MEYETLTLGD MIRRSGGHSR KIPRPKPAPL TAEIQQKILH LPTSWDWRNV
HGINFVSPVR NQASCGSCYS FASMGMLEAR IRILTNNSQT PILSPQEVVS CSQYAQGCEG
GFPYLIAGKY AQDFGLVEEA CFPYTGTDSP CKMKEDCFRY YSSEYHYVGG FYGGCNEALM
KLELVHHGPM AVAFEVYDDF LHYKKGIYHH TGLRDPFNPF ELTNHAVLLV GYGTDSASGM
DYWIVKNSWG TGWGENGYFR IRRGTDECAI ESIAVAATPI PKL*

mutated AA sequence

speed

0.98 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