ClinVar Miner

Submissions for variant NM_005529.7(HSPG2):c.12874G>A (p.Glu4292Lys)

gnomAD frequency: 0.00135  dbSNP: rs141280063
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000711912 SCV000233243 uncertain significance not provided 2014-06-23 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000711912 SCV000842323 likely benign not provided 2017-11-17 criteria provided, single submitter clinical testing
Invitae RCV000711912 SCV001057025 benign not provided 2023-12-30 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001101422 SCV001258027 benign Lethal Kniest-like syndrome 2017-04-27 criteria provided, single submitter clinical testing 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, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.
Illumina Laboratory Services, Illumina RCV001101423 SCV001258028 benign Schwartz-Jampel syndrome 2017-04-27 criteria provided, single submitter clinical testing 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, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000711912 SCV001472330 uncertain significance not provided 2019-08-02 criteria provided, single submitter clinical testing The HSPG2 c.12874G>A; p.Glu4292Lys variant (rs141280063) is reported in the literature in an individual with idiopathic scoliosis (Baschal 2014), though, to our knowledge, it has not been described in association with a congenital skeletal dysplasia. This variant is found in the Finnish European population with an overall allele frequency of 0.98% (243/24858 alleles) in the Genome Aggregation Database. The glutamate at codon 4292 is weakly conserved and computational analyses (SIFT: tolerate, PolyPhen-2: damaging) predict conflicting effects of this variant on protein structure/function. However, given the lack of clinical and functional data, the significance of the p.Glu4292Lys variant is uncertain at this time. References: Baschal EE et al. Exome sequencing identifies a rare HSPG2 variant associated with familial idiopathic scoliosis. G3 (Bethesda). 2014 Dec 12;5(2):167-74
GeneDx RCV000711912 SCV001793163 likely benign not provided 2019-12-24 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 30753492, 25504735)

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