ClinVar Miner

Submissions for variant NM_024675.4(PALB2):c.3501_3502insTGGCCGGGCGCGGTGGCTCACGCCTGTAGTCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCATGAGGTCAGGAGATCGAGACCATCCTGGCTAACAAGGTGAAACCCCNNNNNNNNNNAAAAAAAAAAAAAAAAAAAAGAAATGGTCGGGTACA (p.Asp1168delinsTrpProGlyAlaValAlaHisAlaCysSerProSerThrLeuGlyGlyArgGlyGlyTrpIleMetArgSerGlyAspArgAspHisProGlyTer)

dbSNP: rs2142252136
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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001384386 SCV001583845 pathogenic Familial cancer of breast 2022-02-28 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Retrotransposon insertions including LINE1 (L1), Alu, and SVA (SINE-VNTR-Alu) have been reported to be disease-causing through disruption of either a coding region or splice site (PMID: 19763152, 20307669, 22406018) and loss-of-function variants in PALB2 are known to be pathogenic (PMID: 17200668, 17200671, 17200672, 24136930, 25099575). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. ClinVar contains an entry for this variant (Variation ID: 1071843). This variant has not been reported in the literature in individuals affected with PALB2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change inserts a large fragment of DNA, likely a transposable element, in exon 13 of the PALB2 gene (c.3501_3502ins?), causing a frameshift at codon 1167 (p.Thr1167fs). The exact size and sequence of the insertion cannot be determined by the current assay. However, the insertion is expected to result in an absent or disrupted protein product.

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