ClinVar Miner

Submissions for variant NM_001261826.3(AP3D1):c.3637G>A (p.Ala1213Thr)

gnomAD frequency: 0.00031  dbSNP: rs201113371
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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 RCV001936777 SCV002219401 uncertain significance not provided 2024-12-05 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 1213 of the AP3D1 protein (p.Ala1213Thr). This variant is present in population databases (rs201113371, gnomAD 0.1%). This variant has not been reported in the literature in individuals affected with AP3D1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1440018). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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.
Fulgent Genetics, Fulgent Genetics RCV002479529 SCV002796884 uncertain significance Hermansky-Pudlak syndrome 10 2022-04-26 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004756325 SCV005348826 uncertain significance AP3D1-related disorder 2024-05-17 no assertion criteria provided clinical testing The AP3D1 c.3637G>A variant is predicted to result in the amino acid substitution p.Ala1213Thr. This variant has been reported in the de novo state in an individual with developmental disorder (Turner et al. 2019. PubMed ID: 31785789. Table S2). This variant is reported in 0.13% 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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