ClinVar Miner

Submissions for variant NM_006031.6(PCNT):c.4109G>A (p.Arg1370Gln)

gnomAD frequency: 0.00032  dbSNP: rs145055342
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000176213 SCV000227829 uncertain significance not provided 2015-04-22 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000765508 SCV000896814 uncertain significance Microcephalic osteodysplastic primordial dwarfism type II 2018-10-31 criteria provided, single submitter clinical testing
Invitae RCV000176213 SCV002300790 uncertain significance not provided 2022-10-05 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 1370 of the PCNT protein (p.Arg1370Gln). This variant is present in population databases (rs145055342, gnomAD 0.1%). This variant has not been reported in the literature in individuals affected with PCNT-related conditions. ClinVar contains an entry for this variant (Variation ID: 195605). 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 glutamine 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.
Revvity Omics, Revvity RCV000765508 SCV003814775 uncertain significance Microcephalic osteodysplastic primordial dwarfism type II 2020-06-19 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003416079 SCV004117195 uncertain significance PCNT-related condition 2023-12-12 criteria provided, single submitter clinical testing The PCNT c.4109G>A variant is predicted to result in the amino acid substitution p.Arg1370Gln. To our knowledge, this variant has not been reported in individuals with PCNT-associated disorders in the literature. This variant is reported in 0.11% of alleles in individuals of European (Finnish) descent in gnomAD, which may be too common to be an undocumented primary cause of disease. Although we suspect this variant may be benign, at this time, its clinical significance is uncertain due to the absence of conclusive functional and genetic evidence.

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