ClinVar Miner

Submissions for variant NM_012431.3(SEMA3E):c.1856G>A (p.Arg619His)

gnomAD frequency: 0.00006  dbSNP: rs140160399
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001360494 SCV001556414 uncertain significance CHARGE syndrome 2022-08-23 criteria provided, single submitter clinical testing 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 output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The histidine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 1052334). This variant has not been reported in the literature in individuals affected with SEMA3E-related conditions. This variant is present in population databases (rs140160399, gnomAD 0.02%). This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 619 of the SEMA3E protein (p.Arg619His).
Fulgent Genetics, Fulgent Genetics RCV002486508 SCV002783710 uncertain significance CHARGE syndrome; Hypogonadotropic hypogonadism 7 with or without anosmia 2021-12-29 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003416260 SCV004106552 uncertain significance SEMA3E-related disorder 2024-07-24 no assertion criteria provided clinical testing The SEMA3E c.1856G>A variant is predicted to result in the amino acid substitution p.Arg619His. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.016% of alleles in individuals of African descent in gnomAD. Although we suspect that this variant may be benign, 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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