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: ENST00000236671
MT speed 0 s - this script 2.283025 s

Results

genesymbol	prediction	probability	model	prediction problem	splicing	ClinVar	amino acid changes	variant type	dbSNP ID	protein length	file
CTSD	disease_causing_automatic	0.999999999999963	simple_aae		affected	0	W383C	single base exchange	rs121912790		show file

Taster files

mutation t@sting

documentation

Prediction

disease causing

Model: simple_aae, prob: 0.999999999999963 (classification due to ClinVar, real probability is shown anyway) (explain)

Summary

amino acid sequence changed
known disease mutation at this position (HGMD CM061696)
known disease mutation: rs17574 (pathogenic)
protein features (might be) affected
splice site changes

hyperlink

analysed issue

analysis result

name of alteration

no title

alteration (phys. location)

chr11:1774823C>GN/A show variant in all transcripts IGV

HGNC symbol

CTSD

Ensembl transcript ID

ENST00000236671

Genbank transcript ID

NM_001909

UniProt peptide

P07339

alteration type

single base exchange

alteration region

CDS

DNA changes

c.1149G>C
cDNA.1282G>C
g.10400G>C

AA changes

W383C Score: 215 explain score(s)

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

383

frameshift

known variant

Reference ID: rs121912790
Allele 'G' was neither found in ExAC nor 1000G.
known disease mutation: rs17574 (pathogenic for Neuronal ceroid lipofuscinosis 10) dbSNP NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM061696)

known disease mutation at this position, please check HGMD for details (HGMD ID CM061696)
known disease mutation at this position, please check HGMD for details (HGMD ID CM061696)

regulatory features

H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
H4K20me1, Histone, Histone 4 Lysine 20 mono-methylation
H3K4me1, Histone, Histone 3 Lysine 4 Mono-Methylation

phyloP / phastCons

	PhyloP	PhastCons
(flanking)	2.611	1
	4.934	1
(flanking)	3.385	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 gained	10406	0.31	mu: AGCGGGCCACTCTGCATCCTGGGCGACGTCTTCATCGGCCG	cctg\|GGCG
Acc gained	10405	0.37	mu: CAGCGGGCCACTCTGCATCCTGGGCGACGTCTTCATCGGCC	tcct\|GGGC

distance from splice site

Kozak consensus sequence altered?

N/A

conservation
protein level for non-synonymous changes

species

match

gene

alignment

Human

383

mutated

not conserved

383

Ptroglodytes

no homologue

Mmulatta

all identical

ENSMMUG00000003874

383

Fcatus

all identical

ENSFCAG00000007823

378

Mmusculus

all identical

ENSMUSG00000007891

381

Ggallus

all identical

ENSGALG00000006613

371

Trubripes

all identical

ENSTRUG00000012591

362

Drerio

all identical

ENSDARG00000057698

369

Dmelanogaster

no homologue

Celegans

all identical

R12H7.2

386

Xtropicalis

all identical

ENSXETG00000024954

305

protein features

start (aa)	end (aa)	feature	details
383	385	STRAND		lost
387	390	HELIX		might get lost (downstream of altered splice site)
393	398	STRAND		might get lost (downstream of altered splice site)
399	402	TURN		might get lost (downstream of altered splice site)
403	409	STRAND		might get lost (downstream of altered splice site)

length of protein

normal

AA sequence altered

yes

position of stopcodon in wt / mu CDS

1239 / 1239

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

413 / 413

position of stopcodon in wt / mu cDNA

1372 / 1372

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

134 / 134

chromosome

strand

-1

last intron/exon boundary

1205

theoretical NMD boundary in CDS

1021

length of CDS

1239

coding sequence (CDS) position

1149

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

1282

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

10400

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

1774823

original gDNA sequence snippet

CCACCCAGCGGGCCACTCTGGATCCTGGGCGACGTCTTCAT

altered gDNA sequence snippet

CCACCCAGCGGGCCACTCTGCATCCTGGGCGACGTCTTCAT

original cDNA sequence snippet

CCACCCAGCGGGCCACTCTGGATCCTGGGCGACGTCTTCAT

altered cDNA sequence snippet

CCACCCAGCGGGCCACTCTGCATCCTGGGCGACGTCTTCAT

wildtype AA sequence

MQPSSLLPLA LCLLAAPASA LVRIPLHKFT SIRRTMSEVG GSVEDLIAKG PVSKYSQAVP
AVTEGPIPEV LKNYMDAQYY GEIGIGTPPQ CFTVVFDTGS SNLWVPSIHC KLLDIACWIH
HKYNSDKSST YVKNGTSFDI HYGSGSLSGY LSQDTVSVPC QSASSASALG GVKVERQVFG
EATKQPGITF IAAKFDGILG MAYPRISVNN VLPVFDNLMQ QKLVDQNIFS FYLSRDPDAQ
PGGELMLGGT DSKYYKGSLS YLNVTRKAYW QVHLDQVEVA SGLTLCKEGC EAIVDTGTSL
MVGPVDEVRE LQKAIGAVPL IQGEYMIPCE KVSTLPAITL KLGGKGYKLS PEDYTLKVSQ
AGKTLCLSGF MGMDIPPPSG PLWILGDVFI GRYYTVFDRD NNRVGFAEAA RL*

mutated AA sequence

speed

0.29 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