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NM_001909.5(CTSD):c.190G>A (p.Glu64Lys)

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Interpretation:
Uncertain significance​

Review status:
criteria provided, single submitter
Submissions:
1 (Most recent: Jan 7, 2021)
Last evaluated:
Mar 1, 2019
Accession:
VCV000575391.3
Variation ID:
575391
Description:
single nucleotide variant
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NM_001909.5(CTSD):c.190G>A (p.Glu64Lys)

Allele ID
570408
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
11p15.5
Genomic location
11: 1761347 (GRCh38) GRCh38 UCSC
11: 1782577 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000011.10:g.1761347C>T
NC_000011.9:g.1782577C>T
NG_008655.1:g.7646G>A
NM_001909.5:c.190G>A MANE Select NP_001900.1:p.Glu64Lys missense
Protein change
E64K
Other names
-
Canonical SPDI
NC_000011.10:1761346:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00040 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00001
The Genome Aggregation Database (gnomAD), exomes 0.00002
Exome Aggregation Consortium (ExAC) 0.00004
1000 Genomes Project 0.00040
Links
dbSNP: rs539823013
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Mar 1, 2019 RCV000697591.3
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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
(Mar 01, 2019)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis
Allele origin: germline
Invitae
Accession: SCV000826211.3
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces glutamic acid with lysine at codon 64 of the CTSD protein (p.Glu64Lys). The glutamic acid residue is weakly conserved and there … (more)

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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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532

Text-mined citations for rs539823013...

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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 08, 2021