ClinVar Miner

Submissions for variant NM_144773.4(PROKR2):c.169G>T (p.Gly57Cys)

gnomAD frequency: 0.00001  dbSNP: rs201283126
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001138033 SCV001298048 likely benign Hypogonadotropic hypogonadism 3 with or without anosmia 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 and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Athena Diagnostics RCV004998662 SCV005620579 uncertain significance not provided 2024-07-03 criteria provided, single submitter clinical testing Available data are insufficient to determine the clinical significance of the variant at this time. The frequency of this variant in the general population is higher than would generally be expected for pathogenic variants in this gene. (http://gnomad.broadinstitute.org) This variant has been seen where an alternate explanation for disease was also identified, suggesting this variant may not cause disease. Polyphen and MutationTaster yielded discordant predictions regarding whether this amino acid change is damaging to the protein.
GeneDx RCV004998662 SCV005870424 uncertain significance not provided 2024-08-22 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 36694982, 38272512, 33983622, 35669683)

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