PALB2 NM_024675.3:c.104T>C, Leu35Pro

This variant is considered likely pathogenic. Functional studies indicate this variant impacts protein function [PMID: 28319063]. This variant is expected to disrupt protein structure [PMID: 19369211].

This missense variant replaces leucine with proline at codon 35 of the PALB2 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). Functional studies have reported that this variant impacts PALB2 function in homolgy-directed DNA repair, BRCA1 binding, PARP inhibitor and cisplatin sensitivity, DNA damage response assays (PMID: 28319063, 31586400, 31757951, 31636395, 33964450, 35853885). This variant has been reported in two unrelated individuals affected with breast cancer including co-segregation with disease from mother to daughter in one family (PMID: 28319063, 32185139). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Although there is a suspicion that this variant may be associated with disease, additional studies are necessary to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

The p.L35P variant (also known as c.104T>C), located in coding exon 2 of the PALB2 gene, results from a T to C substitution at nucleotide position 104. The leucine at codon 35 is replaced by proline, an amino acid with similar properties. A functional assay demonstrated that p.L35P results in defects in activation and maintenance of the G2/M cell cycle checkpoint, which is involved in regulating response to DNA damage from ionizing radiation (Simhadri S et al. Oncogene, 2019 03;38:1585-1596). Additionally, functional assays have demonstrated that this alteration disrupts homlogy directed repair activity, confers sensitivity to PARP inhibitors, reduces RAD51 foci formation in response to DNA damage, and significantly diminshes complex formation with BRCA1 and BRCA2 (Wiltshire T et al. Genet. Med., 2019 Oct; Boonen RACM et al. Nat Commun, 2019 Nov;10:5296; Foo TK et al. Oncogene, 2017 07;36:4161-4170). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is still limited at this time, the clinical significance of this alteration remains unclear.

This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 35 of the PALB2 protein (p.Leu35Pro). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with breast cancer (PMID: 28319063). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 657328). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects PALB2 function (PMID: 28319063, 30337689, 31586400, 31636395, 31757951, 33169439, 33964450). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.