ClinVar Miner

Submissions for variant NM_005529.7(HSPG2):c.3010T>A (p.Ser1004Thr)

gnomAD frequency: 0.00002  dbSNP: rs775214455
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001811705 SCV002049363 uncertain significance not provided 2021-07-16 criteria provided, single submitter clinical testing The HSPG2 c.3010T>A; p.Ser1004Thr variant (rs775214455), to our knowledge, is not reported in the medical literature or gene specific databases. This variant is only observed on five alleles in the Genome Aggregation Database, indicating it is not a common polymorphism. The serine at codon 1004 is moderately conserved, and computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.346). Due to limited information, the clinical significance of this variant is uncertain at this time.
Labcorp Genetics (formerly Invitae), Labcorp RCV001811705 SCV003286531 uncertain significance not provided 2022-06-03 criteria provided, single submitter clinical testing This variant is present in population databases (rs775214455, gnomAD 0.004%). This sequence change replaces serine, which is neutral and polar, with threonine, which is neutral and polar, at codon 1004 of the HSPG2 protein (p.Ser1004Thr). This variant has not been reported in the literature in individuals affected with HSPG2-related conditions. 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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 1330525).
Ambry Genetics RCV002542335 SCV003635527 uncertain significance Inborn genetic diseases 2022-01-26 criteria provided, single submitter clinical testing The c.3010T>A (p.S1004T) alteration is located in exon 23 (coding exon 23) of the HSPG2 gene. This alteration results from a T to A substitution at nucleotide position 3010, causing the serine (S) at amino acid position 1004 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
GeneDx RCV001811705 SCV004170661 uncertain significance not provided 2023-04-20 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

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