ClinVar Miner

Submissions for variant NM_005529.7(HSPG2):c.5891G>A (p.Arg1964Lys)

gnomAD frequency: 0.00014  dbSNP: rs373448635
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics RCV000992141 SCV001144173 uncertain significance not provided 2019-01-28 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000992141 SCV003781058 uncertain significance not provided 2021-12-25 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with lysine, which is basic and polar, at codon 1964 of the HSPG2 protein (p.Arg1964Lys). This variant is present in population databases (rs373448635, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with HSPG2-related conditions. ClinVar contains an entry for this variant (Variation ID: 804904). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The lysine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Revvity Omics, Revvity RCV000992141 SCV003809421 uncertain significance not provided 2019-06-10 criteria provided, single submitter clinical testing
Ambry Genetics RCV003353107 SCV004054302 uncertain significance Inborn genetic diseases 2023-06-16 criteria provided, single submitter clinical testing The c.5891G>A (p.R1964K) alteration is located in exon 46 (coding exon 46) of the HSPG2 gene. This alteration results from a G to A substitution at nucleotide position 5891, causing the arginine (R) at amino acid position 1964 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV000992141 SCV001797966 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000992141 SCV001966440 likely benign not provided no assertion criteria provided clinical testing

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