ClinVar

Description

The PALB2 c.2835-?_3113+?del variant (chr16:23632683_23634451del GRCh37) results in a in frame deletion of exons 9-10, although the precise breakpoints of this deletion were not determined, nor were the effects of this variant on the resulting mRNA or protein product determined. The PALB2 variant was identified in 1 of 818 proband chromosomes (frequency: 0.001) from individuals or families with breast cancer and was not identified in 2452 control chromosomes from healthy individuals (Janatova 2013). The proband of the above family was reported to have breast cancer at age 42 and to have two affected family members, one with breast cancer at age 52, the other at age 40. Studies have displayed that the WD40 domains at the C-terminus of PALB2 (residues 850-1186) are necessary for binding of BRCA2; deletions of this region abolish binding and missense variants disrupt binding (Sy 2009, Park 2014). The variant was identified in ClinVar classified as Likely Pathogenic by Invitae. The variant was not identified in dbSNP, or LOVD 3.0. The variant was not identified in the following control databases: the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). This variant is an in-frame deletion; the impact of this alteration on PALB2 protein function is not known. Deletion of exons 9 and 10 would disrupt the WD40 domain and there is evidence to suggest that the WD-40 domain is essential for PALB2 binding to BRCA2, likely affecting PALB2 function. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more pathogenic role for this variant. This variant is classified as likely pathogenic.