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NM_001909.5(CTSD):c.154G>A (p.Val52Ile)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(3);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Oct 1, 2021)
Last evaluated:
Nov 27, 2020
Accession:
VCV000205335.8
Variation ID:
205335
Description:
single nucleotide variant
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NM_001909.5(CTSD):c.154G>A (p.Val52Ile)

Allele ID
202549
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11p15.5
Genomic location
11: 1761383 (GRCh38) GRCh38 UCSC
11: 1782613 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.10:g.1761383C>T
NC_000011.9:g.1782613C>T
NG_008655.1:g.7610G>A
NM_001909.5:c.154G>A MANE Select NP_001900.1:p.Val52Ile missense
Protein change
V52I
Other names
p.V52I:GTC>ATC
Canonical SPDI
NC_000011.10:1761382:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00025
The Genome Aggregation Database (gnomAD) 0.00026
The Genome Aggregation Database (gnomAD), exomes 0.00028
1000 Genomes Project 0.00040
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00023
Exome Aggregation Consortium (ExAC) 0.00034
Links
ClinGen: CA314312
dbSNP: rs143517230
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Aug 16, 2016 RCV000716724.1
Likely benign 1 criteria provided, single submitter Nov 27, 2020 RCV000862792.3
Uncertain significance 1 criteria provided, single submitter Apr 27, 2017 RCV001108795.1
Likely benign 1 criteria provided, single submitter Nov 3, 2020 RCV001721192.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CTSD - - GRCh38
GRCh37
377 410

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis 10
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001266076.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Aug 16, 2016)
criteria provided, single submitter
Method: clinical testing
Seizures
Allele origin: germline
Ambry Genetics
Accession: SCV000847567.2
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Insufficient or conflicting evidence
Likely benign
(Nov 27, 2020)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis
Allele origin: germline
Invitae
Accession: SCV001003345.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Nov 03, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000240873.13
Submitted: (Oct 01, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs143517230...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 16, 2021