ClinVar Miner

Submissions for variant NM_006031.6(PCNT):c.5479G>A (p.Ala1827Thr)

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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 RCV002993569 SCV003291508 uncertain significance not provided 2021-12-23 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 1827 of the PCNT protein (p.Ala1827Thr). This variant is present in population databases (rs563470468, gnomAD 0.2%). This variant has not been reported in the literature in individuals affected with PCNT-related conditions. 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 threonine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.
Ambry Genetics RCV004065180 SCV005002882 uncertain significance Inborn genetic diseases 2023-03-13 criteria provided, single submitter clinical testing The c.5479G>A (p.A1827T) alteration is located in exon 28 (coding exon 28) of the PCNT gene. This alteration results from a G to A substitution at nucleotide position 5479, causing the alanine (A) at amino acid position 1827 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
PreventionGenetics, part of Exact Sciences RCV003936484 SCV004751993 likely benign PCNT-related disorder 2022-05-11 no assertion criteria provided clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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