ClinVar Miner

Submissions for variant NM_006080.3(SEMA3A):c.1372G>A (p.Val458Ile)

gnomAD frequency: 0.00004  dbSNP: rs553661856
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV004591567 SCV005078556 uncertain significance not provided 2023-09-15 criteria provided, single submitter clinical testing Identified in a patient with Kallmann syndrome in published literature (Dai et al., 2020); In silico analysis supports that this missense variant does not alter protein structure/function; Variants in candidate genes are classified as variants of uncertain significance in accordance with ACMG guidelines (Richards et al., 2015); This variant is associated with the following publications: (PMID: 32060892, 36517585)
OMIM RCV001785417 SCV002026472 risk factor Hypogonadotropic hypogonadism 16 with or without anosmia 2021-11-22 no assertion criteria provided literature only
PreventionGenetics, part of Exact Sciences RCV004749740 SCV005365729 uncertain significance SEMA3A-related disorder 2024-03-15 no assertion criteria provided clinical testing The SEMA3A c.1372G>A variant is predicted to result in the amino acid substitution p.Val458Ile. This variant has been reported in an individual with isolated hypogonadotropic hypogonadism; in addition, functional studies suggested that the p.Val458Ile change prevented extracellular secretion of SEMA3A protein (Dai et al. 2020. PubMed ID: 32060892). This variant is reported in 0.020% of alleles in individuals of South Asian descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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