Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PP3_Strong
The NM_007294.4(BRCA1):c.83T>C(p.Leu28Pro) variant causes a missense, splice region change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L28Q) has been classified as Uncertain significance.
BRCA1 (HGNC:1100): (BRCA1 DNA repair associated) This gene encodes a 190 kD nuclear phosphoprotein that plays a role in maintaining genomic stability, and it also acts as a tumor suppressor. The BRCA1 gene contains 22 exons spanning about 110 kb of DNA. The encoded protein combines with other tumor suppressors, DNA damage sensors, and signal transducers to form a large multi-subunit protein complex known as the BRCA1-associated genome surveillance complex (BASC). This gene product associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. This protein thus plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. Alternative splicing plays a role in modulating the subcellular localization and physiological function of this gene. Many alternatively spliced transcript variants, some of which are disease-associated mutations, have been described for this gene, but the full-length natures of only some of these variants has been described. A related pseudogene, which is also located on chromosome 17, has been identified. [provided by RefSeq, May 2020]
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
PM1
In a hotspot region, there are 8 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 3 benign, 17 uncertain in NM_007294.4
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.969
Uncertain significance, criteria provided, single submitter
clinical testing
Color Diagnostics, LLC DBA Color Health
Aug 02, 2022
This missense variant replaces leucine with proline at codon 28 in the RING domain of the BRCA1 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have reported that this variant disrupted BRCA1 function in homology-directed DNA repair, a haploid cell proliferation, mammalian two-hybrid assay for BARD1 binding and E3 ubiquitin ligase assays, albeit the degrees of the disruption were often not as severe as the null controls (PMID: 16403807, 25823446, 30209399, 35659930). This variant has been reported in at least one individual or family affected with breast and/or ovarian cancer (PMID: 18779604). A multifactorial analysis has reported likelihood ratios for pathogenicity based on co-occurrence and family history of 1.0673 and 0.3838, respectively (PMID: 31131967). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Although there is a suspicion that this variant may be associated with disease based on functional evidence, there is insufficient clinical data to be conclusive. Therefore, this variant is classified as a Variant of Uncertain Significance. -
Likely pathogenic, criteria provided, single submitter
clinical testing
Ambry Genetics
Sep 15, 2022
The p.L28P variant (also known as c.83T>C), located in coding exon 2 of the BRCA1 gene, results from a T to C substitution at nucleotide position 83. The leucine at codon 28 is replaced by proline, an amino acid with similar properties. One functional study found that this nucleotide substitution is deleterious in a high throughput genome editing haploid cell survival assay (Findlay GM et al. Nature, 2018 10;562:217-222). However, functional assays on RING domain variants to measure BRCA1 E3 ubiquitin ligase activity and binding to BARD1 indicate unknown significance of this alteration (Starita LM et al. Genetics, 2015 Jun;200:413-22; Caleca L et al. Cancers (Basel), 2019 Jan;11). Based on internal structural analysis, this variant is anticipated to result in a significant decrease in structural stability (Internal Ambry Data; Morris JR et al. Hum. Mol. Genet., 2006 Feb;15:599-606). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter
clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Dec 27, 2021
Variant summary: BRCA1 c.83T>C (p.Leu28Pro) results in a non-conservative amino acid change located in the Zinc finger, RING-type domain (IPR001841) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. Based on a combination of a multiple sequence alignment of orthologous BRCA1 sequences and a measure of the chemical difference between the amino acids present in the sequence alignment, this variant has been predicted to be likely deleterious and fully conserved across species (Abkevich_2004). The variant was absent in 250258 control chromosomes. Although this variant has been reported in various databases (HGMD, LOVD, UMD and BIC), to our knowledge, no occurrence of c.83T>C in individuals affected with Hereditary Breast And Ovarian Cancer Syndrome has been reported. Several publications report experimental evidence evaluating an impact on protein function (example, Morris_2006, Starita_2015, Findlay_2018). The most pronounced variant effect results in a reproducible loss of homology directed repair (HDR) activity as well as a reduction in the E3 ubiquitin ligase activity of BRCA1. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as uncertain significance. Some submitters cite overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic. -
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter
clinical testing
GeneDx
Jun 21, 2016
This variant is denoted BRCA1 c.83T>C at the cDNA level, p.Leu28Pro (L28P) at the protein level, and results in the change of a Leucine to a Proline (CTG>CCG). Using alternate nomenclature, this variant would be defined as BRCA1 202T>C. This variant was observed in at least one individual with a personal and/or family history suspicious for Hereditary Breast and Ovarian Cancer (Kurian 2008). BRCA1 Leu28Pro was evaluated by yeast two-hybrid assay to have intact BARD1 and E3 binding, but reduced E3 ligase activity (Morris 2006). BRCA1 Leu28Pro was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, suggesting it is not a common benign variant in these populations. Since Leucine and Proline differ in some properties, this is considered a semi-conservative amino acid substitution. BRCA1 Leu28Pro occurs at a position that is conserved in mammals and is located in the ring figure domain and a region known to interact with multiple other proteins (Paul 2014). In silico analyses predict that this variant is probably damaging to protein structure and function. Based on currently available evidence, it is unclear whether BRCA1 Leu28Pro is a pathogenic or benign variant. We consider it to be a variant of uncertain significance. -
Hereditary breast ovarian cancer syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter
clinical testing
Invitae
Jun 13, 2022
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies have shown that this missense change affects BRCA1 function (PMID: 16403807, 25823446, 30209399). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 55732). This missense change has been observed in individual(s) with clinical features of BRCA1-related conditions (PMID: 10923033, 21520333). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 28 of the BRCA1 protein (p.Leu28Pro). -
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