TP53 p.Pro13Ser

The NM_000546.6(TP53):c.37C>T variant in TP53 is a missense variant predicted to cause substitution of proline by serine at amino acid 13 (p.Pro13Ser). This variant has been reported in 4 unrelated probands meeting Revised Chompret criteria. Based on this evidence, this variant scores 2 total points meeting the TP53 VCEP phenotype scoring criteria of 2-3.5 points. (PS4_Moderate; Internal lab contributors). At least one individual with this variant was found to have a variant allele fraction of 5-35%, which is a significant predictor of variant pathogenicity (PP4, PMID: 34906512, Internal lab contributor). This variant has been observed in 3 heterozygous unrelated females from the same data source with no personal history of cancer prior to age 60 years and no personal history of sarcoma at any age (BS2_Supporting; Internal lab contributor). This variant has an allele frequency of 0.000001239 (2/1613918 alleles) across gnomAD v4.1.0 which is lower than the Clingen TP53 VCEP threshold (<0.00003) for PM2_Supporting and has a subpopulation allele frequency of <0.00004 in all non-bottleneck populations with 2 or more alleles present (PM2_Supporting). In vitro assays performed in yeast and/or human cell lines showed functional transactivation and retained growth suppression activity by the majority of available assays indicating that this variant does not impact protein function (BS3; PMIDs: 12826609, 30224644). Computational predictor scores (BayesDel = 0.123287; Align GVGD Class C0) are below the recommended thresholds (BayesDel < 0.16 and > -0.008 and an Align GVGD Class ≤ 55), evidence that does not predict a damaging effect on TP53 via protein change. SpliceAI predicts that the variant has no impact on splicing (BP4). Although this variant meets the criteria to be classified as Likely Benign, the VCEP has overridden this classification to variant of uncertain significance for Li Fraumeni syndrome due to conflicting evidence: BS3, BP4, PM2_supporting, PS4_moderate, PP4, BS2_Supporting. (Bayesian Points: -2; VCEP specifications version 2.4)