ClinVar Genomic variation as it relates to human health

The BRIP1 c.3240dupT (p.Ala1081CysfsTer5) variant results in a frameshift and is predicted to result in premature termination of the protein. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found based on this search. The variant is reported at a frequency of 0.00012 in the East Asian population from the Exome Aggregation Consortium but this is based on one allele in a region of good sequence coverage so the variant is presumed to be rare. Based on the variant frequency, disease prevalence, disease penetrance, and inheritance mode, this variant could not be ruled out of causing disease. Due to the potential impact of frameshift variants and the lack of clarifying evidence, the p.Ala1081CysfsTer5 variant is classified as a variant of unknown significance but suspicious for pathogenicity for BRIP1-related disorders. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

This duplication of one nucleotide in BRIP1 is denoted c.3240dupT at the cDNA level and p.Ala1081CysfsX5 (A1081CfsX5) at the protein level. The normal sequence, with the base that is duplicated in brackets, is TTGA[dupT]GCCA. The duplication causes a frameshift which changes an Alanine to a Cysteine at codon 1081, and creates a premature stop codon at position 5 of the new reading frame. Due to the position of the variant, nonsense mediated decay is not expected to occur, but the variant might cause loss of normal protein function through protein truncation.?? The disrupted region at the end of the gene is not located in a known functional domain. This variant has been reported in at least one individual with sarcoma, who also carried BRIP1 Glu767Asp (Ballinger 2016). Based on currently available evidence, it is unclear whether this duplication is a pathogenic variant or a benign variant. We consider it to be a variant of uncertain significance.

This variant inserts 1 nucleotide in exon 20 of the BRIP1 gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. The truncated protein is expected to disrupt the TopBP1 binding domain (a.a. 1106-1178) and an acetylation site (p.Lys1249) in the C-terminus, which have been reported to play an important role in DNA replication-stress response and maintaining genomic stability (PMID: 20159562, 21127055, 22792074). This variant has been reported in individuals affected with sarcoma, prostate cancer, and bilateral breast cancer (PMID: 27498913, 31214711, 32566746). This variant has been identified in 1/251228 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of BRIP1 function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Likely Pathogenic.

Variant summary: BRIP1 c.3240dupT (p.Ala1081CysfsX5, in last exon) results in a premature termination codon, predicted to cause a truncation of the encoded protein and is not prone to nonsense mediated decay. The variant allele was found at a frequency of 6.1e-05 in 313543 control chromosomes (gnomAD and publication data). This frequency is not significantly higher than estimated for a pathogenic variant in BRIP1 causing Breast Cancer (6.1e-05 vs 6.3e-05), allowing no conclusion about variant significance. c.3240dupT has been reported in the literature in individuals affected with Breast Cancer, Prostate Cancer and Gastric cancer (Kaneyasu_2020, Momozawa_2020, Suzuki_2020, Akamatsu_2022) as well as in controls (Momozawa_2020, Okawa_2023). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Ten submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 and classified this variant as uncertain significance (n=5), likely pathogenic (n=4) and pathogenic (n=1). Based on the evidence outlined above, the variant was classified as likely pathogenic.

This sequence change creates a premature translational stop signal (p.Ala1081Cysfs*5) in the BRIP1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 169 amino acid(s) of the BRIP1 protein. This variant is present in population databases (rs779741278, gnomAD 0.01%). This premature translational stop signal has been observed in individual(s) with sarcoma and prostate cancer (PMID: 27498913, 31214711). ClinVar contains an entry for this variant (Variation ID: 324348). This variant disrupts the TopBP1-binding region of the BRIP1 protein, which plays a critical role in RPA chromatin loading and the activation of the replication checkpoint in response to DNA damage (PMID: 20159562, 21127055). While functional studies have not been performed to directly test the effect of this variant on BRIP1 protein function, this suggests that disruption of this region of the protein is causative of disease. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

The c.3240dupT variant, located in coding exon 19 of the BRIP1 gene, results from a duplication of T at nucleotide position 3240, causing a translational frameshift with a predicted alternate stop codon (p.A1081Cfs*5). This stop codon occurs near the 3' terminus of BRIP1, is not expected to trigger nonsense-mediated mRNA decay, and removes the last 165 amino acids of the protein. The exact functional impact of these removed amino acids is unknown at this time; however, structural and functional analysis suggest that at least two residues contained in this deleted region (Ser1237 and Lys1249) have functional importance (Olsen JV et al. Sci Signal. 2010 Jan;3:ra3; Xie J et al. PLoS Genet. 2012 Jul;8:e1002786). This alteration was detected in a patient diagnosed with bilateral breast cancer at age 47, her mother, who was diagnosed with breast cancer at age 70, and a maternal aunt, who was diagnosed with breast cancer at ages 58 and 70 (Kaneyasu T et al. NPJ Breast Cancer. 2020 Jun;6:25). This alteration has also been detected in a cohort of 549 Japanese men with prostate cancer (Kimura H et al. Br J Cancer, 2022 Nov;127:1680-1690). Based on the majority of available evidence to date, this variant is likely to be pathogenic.

This variant is classified as a variant of uncertain significance as there is insufficient evidence to determine its impact on protein function and/or cancer risk.

Curator: Arleen D. Auerbach. Submitter to LOVD: Yukihide Momozawa.