ClinVar Genomic variation as it relates to human health

Variant allele predicted to encode a truncated non-functional protein.

Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; Not observed at significant frequency in large population cohorts (gnomAD); Observed in individuals with a personal or family history consistent with pathogenic variants in this gene (Walsh et al., 2011; Kluska et al., 2015); Also known as 4471G>T; This variant is associated with the following publications: (PMID: 34413315, 22006311, 25948282, 28678401, 29446198, 30322717, AlHinai2021[CaseReport], 31853058, 32377563)

This variant changes 1 nucleotide in exon 11 of the BRCA2 gene, creating a premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. This variant has been observed in multiple individuals affected with breast, ovarian and fallopian tube cancer (PMID: 22006311, 30322717, 33471991; Leiden Open Variation Database DB-ID BRCA2_002639; Color internal data). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of BRCA2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.

This variant changes 1 nucleotide in exon 11 of the BRCA2 gene, creating a premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. To our knowledge, functional studies have not been reported for this variant. This variant has been observed in 5 individuals affected with breast, ovarian and fallopian tube cancer (PMID: 22006311, 30322717, 33471991; Leiden Open Variation Database DB-ID BRCA2_002639; Color internal data). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of BRCA2 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic.

Variant summary: BRCA2 c.4243G>T (p.Glu1415X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. This variant is also known as 4471G>T.Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant was absent in 242558 control chromosomes (gnomAD). c.4243G>T has been reported in the literature in individuals affected with hereditary breast cancer, ovarian cancer, fallopian tube carcinoma, head and neck squamous cell carcinoma (examples: Walsh_2011, Chandrasekharappa_2017, Carter_2018, and Rebbeck_2018). These data indicate that the variant is very likely to be associated with disease. Ten submitters including an expert panel (ENIGMA) have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

This sequence change creates a premature translational stop signal (p.Glu1415*) in the BRCA2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in BRCA2 are known to be pathogenic (PMID: 20104584). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with fallopian tube carcinoma or head and neck squamous cell carcinoma (PMID: 22006311, 28678401). This variant is also known as c.4471G>T (p.Glu1416X). ClinVar contains an entry for this variant (Variation ID: 37890). For these reasons, this variant has been classified as Pathogenic.

The p.E1415* pathogenic mutation (also known as c.4243G>T), located in coding exon 10 of the BRCA2 gene, results from a G to T substitution at nucleotide position 4243. This changes the amino acid from a glutamic acid to a stop codon within coding exon 10. This alteration has been previously reported in individuals diagnosed with ovarian cancer (Walsh T et al. Proc. Natl. Acad. Sci. U.S.A. 2011 Nov;108:18032-7; Carter NJ et al. Gynecol. Oncol., 2018 12;151:481-488) and in an individual diagnosed with a head and neck squamous cell cancer (Chandrasekharappa SC et al. Cancer, 2017 Oct;123:3943-3954). This alteration was also identified in a large, worldwide study of BRCA1/2 mutation positive families (Rebbeck TR et al. Hum. Mutat., 2018 05;39:593-620). Of note, this alteration is also designated as "4471G>T" in published literature. In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.