ClinVar Genomic variation as it relates to human health

This variant is considered likely benign. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 25085752].

Variant summary: PALB2 c.194C>T (p.Pro65Leu) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 4.8e-05 in 251470 control chromosomes, predominantly at a frequency of 9.7e-05 within the Non-Finnish European subpopulation in the gnomAD database. However, the variant was observed in the North-western European subpopulation with an even higher allele frequency, 0.00017 (i.e. 7/42220 alleles), and this frequency is similar to the estimated maximal expected allele frequency for a pathogenic variant in PALB2 causing Hereditary Breast and Ovarian Cancer phenotype (0.00016), suggesting that the variant might be a benign polymorphism. The variant, c.194C>T, has been reported in the literature in individuals affected with breast cancer and other tumor phenotypes, however it was also reported in several healthy controls (e.g. Adank_2011, Bodian_2014, Zhen_2015, Yurgelun_2015, Thompson_2015, Ramus_2015, Damiola_2015, Decker_2017, Hauke_2018). These reports do not provide unequivocal conclusions about association of the variant with Breast Cancer. However, in a recent large study evaluating breast cancer cases and controls in the Breast Cancer Association Consortium (BCAC), the variant was reported in 12/60466 cases, but was also found in 11/53461 controls, suggesting no increased relative risk for breast cancer development (Dorling_2021 through LOVD). In addition, at least one publication reported experimental evidence evaluating an impact on protein function, and demonstrated that the variant protein had BRCA1-binding similar to wild-type, and had normal function in a drug sensitivity (PARP inhibitor) assay (Rodrigue_2019). The following publications have been ascertained in the context of this evaluation (PMID: 20582465, 24728327, 26564480, 33471991, 29522266, 33139182, 26315354, 31586400, 26283626, 25980754, 25356972, 35264596, 28779002). Thirteen submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as likely benign (n=2) and VUS (n=11). Based on the evidence outlined above, the variant was classified as likely benign.

The frequency of this variant in the general population, 0.000093 (12/129184 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported in families with breast, ovarian or pancreatic cancer (PMID: 20582465 (2011)), individuals with breast cancer (PMID: 28779002 (2017), 26564480 (2015), 35264596 (2022)), ovarian cancer (PMID: 26315354 (2015), 32546565 (2021)), pancreatic cancer (PMID: 25356972 (2015)), Lynch syndrome (PMID: 25980754 (2015)) and in unaffected controls (PMID: 28779002 (2017), 26283626 (2015)). In a large scale breast cancer association study, the variant was found in both breast cancer cases as well as in unaffected individuals (PMID: 33471991 (2021), see also LOVD (http://databases.lovd.nl/shared/genes/PALB2)). Functional studies found that this variant performed similar to wild type and showed normal function in a PARP inhibitor assay (PMID: 31586400 (2019)), and also showed little functional impact in BRCA2 binding and recruitment kinetics assays (PMID: 33139182 (2021)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is benign. Based on the available information, we are unable to determine the clinical significance of this variant.

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

Observed in individuals with PALB2-related and other cancers, but also in healthy controls (PMID: 20582465, 25356972, 26564480, 26315354, 26283626, 25980754, 28779002, 29522266, 32546565, 35264596, 36605468); Published functional studies suggest no damaging effect: PARP inhibitor sensitivity and BRCA1 interaction comparable to wild type (PMID: 31586400); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 20582465, 24728327, 25356972, 26283626, 26564480, 25980754, 28779002, 26315354, 29522266, 33471991, 32546565, 20871615, 19369211, 35264596, 36605468, 31586400)

PALB2: BP4

This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 65 of the PALB2 protein (p.Pro65Leu). 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 missense change has been observed in individual(s) with breast, ovarian, and/or pancreatic cancer (PMID: 20582465, 25356972, 26315354, 26564480, 35264596). This missense change has been observed to co-occur in individuals with a different variant in PALB2 that has been determined to be pathogenic (Invitae), but the significance of this finding is unclear. ClinVar contains an entry for this variant (Variation ID: 128124). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The leucine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. Experimental studies have shown that this missense change does not substantially affect PALB2 function (PMID: 31586400). 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.

Curators: Marc Tischkowitz, Arleen D. Auerbach. Submitter to LOVD: Marc Tischkowitz.