ClinVar Miner

Submissions for variant NM_001122630.2(CDKN1C):c.97C>T (p.Arg33Cys)

gnomAD frequency: 0.00001  dbSNP: rs956525226
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001047905 SCV001211889 uncertain significance Beckwith-Wiedemann syndrome 2025-01-29 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 44 of the CDKN1C protein (p.Arg44Cys). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with CDKN1C-related conditions. ClinVar contains an entry for this variant (Variation ID: 844933). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt CDKN1C protein function with a negative predictive value of 80%. 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.
St. Jude Molecular Pathology, St. Jude Children's Research Hospital RCV001047905 SCV002584690 uncertain significance Beckwith-Wiedemann syndrome 2022-10-04 criteria provided, single submitter clinical testing The CDKN1C c.130C>T (p.Arg44Cys) missense change has a maximum subpopulation frequency of 0.0098% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org). The in silico tool REVEL is inconclusive about a pathogenic or benign effect of this variant on protein function, and to our knowledge functional studies have not been performed. To our knowledge, this variant has not been reported in individuals with Beckwith-Wiedemann syndrome or IMAGE syndrome. In summary, the evidence currently available is insufficient to determine the clinical significance of this variant. It has therefore been classified as of uncertain significance.
Fulgent Genetics, Fulgent Genetics RCV002481939 SCV002787309 uncertain significance Beckwith-Wiedemann syndrome; IMAGe syndrome 2022-01-11 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV003145290 SCV003831535 uncertain significance not provided 2022-07-21 criteria provided, single submitter clinical testing

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