ClinVar Miner

Submissions for variant NM_022356.4(P3H1):c.1504G>C (p.Gly502Arg)

gnomAD frequency: 0.00103  dbSNP: rs139259804
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000489750 SCV000576805 uncertain significance not provided 2017-12-18 criteria provided, single submitter clinical testing The G502R variant has not been published in association with a LEPRE1-related skeletal dysplasia. The G502R variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The G502R variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. In summary, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Labcorp Genetics (formerly Invitae), Labcorp RCV000538652 SCV000646154 likely benign Osteogenesis imperfecta type 8 2025-01-27 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000538652 SCV000894858 uncertain significance Osteogenesis imperfecta type 8 2018-10-31 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001097772 SCV001254081 uncertain significance Osteogenesis Imperfecta, Recessive 2017-04-27 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Illumina Laboratory Services, Illumina RCV000538652 SCV001254082 uncertain significance Osteogenesis imperfecta type 8 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000538652 SCV001471768 uncertain significance Osteogenesis imperfecta type 8 2020-01-28 criteria provided, single submitter clinical testing The P3H1 c.1504G>C; p.Gly502Arg variant (rs139259804), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 426382). This variant is found in the general population with an overall allele frequency of 0.095% (270/282864 alleles) in the Genome Aggregation Database. The glycine at codon 502 is moderately conserved, and/ computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Due to limited information, the clinical significance of the p.Gly502Arg variant is uncertain at this time.
Revvity Omics, Revvity RCV000538652 SCV003816564 uncertain significance Osteogenesis imperfecta type 8 2021-11-16 criteria provided, single submitter clinical testing

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