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NM_003383.5(VLDLR):c.982A>G (p.Ser328Gly)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Likely benign(1);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
4 (Most recent: Mar 14, 2019)
Last evaluated:
Jun 8, 2018
Accession:
VCV000373721.2
Variation ID:
373721
Description:
single nucleotide variant
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NM_003383.5(VLDLR):c.982A>G (p.Ser328Gly)

Allele ID
359931
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
9p24.2
Genomic location
9: 2643875 (GRCh38) GRCh38 UCSC
9: 2643875 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000009.11:g.2643875A>G
NC_000009.12:g.2643875A>G
NM_003383.5:c.982A>G MANE Select NP_003374.3:p.Ser328Gly missense
... more HGVS
Protein change
S328G, S287G
Other names
-
Canonical SPDI
NC_000009.12:2643874:A:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00220 (G)

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00049
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00223
Trans-Omics for Precision Medicine (TOPMed) 0.00233
The Genome Aggregation Database (gnomAD) 0.00207
1000 Genomes Project 0.00220
Exome Aggregation Consortium (ExAC) 0.00064
Links
ClinGen: CA4964697
dbSNP: rs116306908
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 Jun 8, 2018 RCV000902106.1
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Dec 14, 2016 RCV000414575.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
VLDLR - - GRCh38
GRCh37
230 447

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Dec 14, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000492341.1
Submitted: (Dec 21, 2016)
Evidence details
Comment:
A variant of uncertain significance has been identified in the VLDLR gene. The S328G variant has not been published as a pathogenic variant, nor has … (more)
Uncertain significance
(Oct 29, 2015)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Genetic Services Laboratory, University of Chicago
Accession: SCV000597861.1
Submitted: (Jul 05, 2017)
Evidence details
Benign
(Nov 17, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000702907.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Jun 08, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001046509.1
Submitted: (Mar 14, 2019)
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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Title Author Journal Year Link
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=VLDLR - - - -

Text-mined citations for rs116306908...

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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 May 27, 2021