ClinVar Genomic variation as it relates to human health

This sequence change falls in intron 12 of the PALB2 gene. It does not directly change the encoded amino acid sequence of the PALB2 protein. RNA analysis indicates that this variant induces altered splicing and likely disrupts the C-terminus of the protein. This variant is present in population databases (rs587782566, gnomAD 0.006%). This variant has been observed in individual(s) with Fanconi anemia (PMID: 30792206). ClinVar contains an entry for this variant (Variation ID: 142586). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in the generation of two aberrant transcripts, one that leads to out-of-frame exon 12 skipping and the other that leads to the in-frame skipping of exons 11 and 12 together and introduces a new termination codon (PMID: 30890586, 32133419; Invitae). However the mRNA is not expected to undergo nonsense-mediated decay. This variant disrupts a region of the PALB2 protein in which other variant(s) (p.Tyr1183*) have been determined to be pathogenic (PMID: 17200671, 20927582, 21165770, 21365267, 26283626, 26296701). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

Variant summary: PALB2 c.3350+5G>A alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. One computational tool predicts the variant weakens a 5' donor site. Experimental evidence from multiple studies demonstrate that this variant affects mRNA splicing leading to aberrant transcripts, most significantly to skipping of exon 12 (Karam_2019, Lopez-Perolio_2019, Mori_2019, Landrith_2020). Some of these studies identified naturally occurring alternative splicing event(s) leading to skipping of exon 12. However, the variant causes a significant increase to the level of alternative splicing resulting in skipping of this exon. The predicted protein encoded by this transcript is unlikely to be functional, as it lacks part of the C-terminal WD40 beta-propeller domain that mediates PALB2 interaction with several key homologous recombination proteins, including BRCA2 and RAD51 (Lopez-Perolio_2019, Landrith_2020). The variant allele was found at a frequency of 8e-06 in 251408 control chromosomes (gnomAD). c.3350+5G>A has been reported in the literature in individuals affected with Hereditary Breast And Ovarian Cancer Syndrome and pancreatic ductal adenocarcinoma (e.g. Kondo_2018, Landrith_2020). It was also reported in a homozygous individual affected with Fanconi Anemia (Mori_2019). Three ClinVar submitters (evaluation after 2014) cite the variant as likely pathogenic and one ClinVar submitter (evaluation after 2014) cites it as uncertain significance. Based on the evidence outlined above, the variant was classified as likely pathogenic.

This variant is considered likely pathogenic. mRNA analysis has demonstrated abnormal mRNA splicing occurs [PMID: 30792206, 32133419, 34846068]. This variant has been observed homozygous in one or more individuals with Fanconi Anemia [PMID: 30792206].

This variant causes a G to A nucleotide substitution at the +5 position of the intron 12 splice donor site of the PALB2 gene. Four RNA studies have reported aberrant mRNA transcripts in variant carriers and in one minigene splicing assay that are predicted to disrupt the BRCA2 and RAD51 binding domain in the protein (PMID: 30792206, 30890586, 32133419, 32238468, 34846068). One of the aberrant transcript is also present in healthy controls, albeit at a lower average level than in carriers with this variant (PMID: 32133419). This variant has been reported in two individuals affected with breast cancer, one individual affected with pancreatic cancer who also has a ATM truncation variant, and another individual affected with ovarian cancer (PMID: 29731985, 34793666, 35676859). The variant also has been observed in a homozygous carrier affected with Fanconi anemia (PMID: 30792206, 32238468). This variant has been identified in 2/251408 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of PALB2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Likely Pathogenic.

The c.3350+5G>A intronic variant results from a G to A substitution 5 nucleotides after coding exon 12 in the PALB2 gene. This nucleotide position is highly conserved in available vertebrate species. This alteration has been identified in the homozygous state in an individual with Fanconi Anemia features and RNA analysis showed skipping of coding exon 12 (Mori M et al. Haematologica. 2019 Oct;104:1962-1973). In silico splice site analysis for this alteration is inconclusive. RNA studies have demonstrated this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). Based on the majority of available evidence to date, this variant is likely to be pathogenic.

The PALB2 c.3350+5G>A variant is predicted to interfere with splicing. This variant has been reported in the homozygous state in an individual with Fanconi anemia (Mori et al 2019. PubMed ID: 30792206). It has also been described in individuals with breast or pancreatic cancer, and two of these individuals also carried a frameshift variant in ATM (Kondo et al. 2018. PubMed ID: 29731985; Megid et al. 2022. PubMed ID: 36003761; Park et al. 2021. PubMed ID: 34793666). RNA studies indicate this variant causes exon 12 skipping (Mori et al. 2019. PubMed ID: 30792206; Lopez-Perolio et al. 2019. PubMed ID: 30890586; Valenzuela-Palomo et al. 2021. PubMed ID: 34846068). This variant is reported in 0.0058% of alleles in individuals of Latino descent in gnomAD and is interpreted as pathogenic or likely pathogenic in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/142586/). This variant is interpreted as likely pathogenic.