ClinVar Miner

Submissions for variant NM_006031.6(PCNT):c.9706C>T (p.Arg3236Ter)

gnomAD frequency: 0.00004  dbSNP: rs757793925
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV000512819 SCV000609067 pathogenic not provided 2022-06-01 criteria provided, single submitter clinical testing PCNT: PVS1, PM2
Invitae RCV000512819 SCV003483900 pathogenic not provided 2024-01-29 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg3236*) in the PCNT gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PCNT are known to be pathogenic (PMID: 18174396, 22821869). This variant is present in population databases (rs757793925, gnomAD 0.01%). 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: 444580). For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV003147495 SCV003836411 likely pathogenic Microcephalic osteodysplastic primordial dwarfism type II 2022-03-22 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003392344 SCV004118877 likely pathogenic PCNT-related condition 2023-06-16 criteria provided, single submitter clinical testing The PCNT c.9706C>T variant is predicted to result in premature protein termination (p.Arg3236*). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.013% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/21-47863728-C-T) and has been classified as pathogenic/likely pathogenic by multiple submitters in ClinVar (https://preview.ncbi.nlm.nih.gov/clinvar/variation/444580/). Nonsense variants in PCNT are expected to be pathogenic. This variant is interpreted as likely pathogenic.

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