ClinVar Genomic variation as it relates to human health

The c.736G>C (p.Ala246Pro) variant in BRAF has been reported in the literature as a de novo occurrence in at least 2 patients with clinical features of a RASopathy (PM6 and PS2; PMID 16474404 and 18042262). In vitro functional studies provide some evidence that the p.Ala246Pro variant may impact protein function (PS3; 16474404, 19376813). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). The variant is located in the BRAF gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID 29493581). This variant is in a location which has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of BRAF (PM1; PMID 29493581). Computational prediction tools and conservation analysis suggest that the p.Ala246Pro variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PP2, PP3, PM1, PM2, PM6, PS2, PS3.

PP2, PP3, PM1, PM2, PM6, PS2, PS3, PS4

Published functional studies demonstrate a damaging effect that the A246P variant results in increased ELK-dependent transcription, leading to activation of BRAF and stimulation of downstream effectors (MEK and ERK) (Niihori et al., 2006); Not observed in large population cohorts (gnomAD); Missense variants in this gene are often considered pathogenic (HGMD); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 19376813, 24409384, 34573299, 30141192, 20523244, 16474404, 18042262, 23885229, 24803665, 28809097, 28911804, 27666661, 31560489, 35418823, 24957944, 15488754, 16439621, 15520807, 17603483, 29493581, 17704260)

The missense c.736G>C (p.Ala246Pro) variant in BRAF gene has been reported in heterozygous state in individuals affected with cardio-facio-cutaneous syndrome or Noonan syndrome (Ohtake A et al., 2011). Experimental studies have shown that this missense increased ELK-dependent transcription, leading to activation of BRAF and stimulation of downstream effectors (MEK and ERK) (Niihori et al., 2006). The p.Ala246Pro variant is novel (not in any individuals) in gnomAD and in 1000 genome database. It has been submitted to ClinVar as Pathogenic. The amino acid Ala at position 246 is changed to a Pro changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Ala246Pro in BRAF is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic.

The p.Ala246Pro variant in BRAF has been reported in 6 individuals with clinical features of Cardio-facio-cutaneous syndrome (CFC) (Niihori 2006, Nava 2007, Nys trom 2008, Schulz 2008, Ohtake 2011). This variant occurred de novo in 2 of thes e individuals (Niihori 2006, Schulz 2008), and one of these individuals also had Non-Hodgkin Lymphoma (Ohtake 2011). Furthermore, this variant has now been iden tified by our laboratory in 5 individuals with clinical features of Noonan syndr ome and/or CFC syndrome. It was also absent from large population studies. There fore, this variant meets our criteria to be classified as pathogenic (http://www .partners.org/personalizedmedicine/LMM).

For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects BRAF function (PMID: 16474404). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt BRAF protein function. ClinVar contains an entry for this variant (Variation ID: 13965). This missense change has been observed in individuals with cardio-facio-cutaneous syndrome or Noonan syndrome (PMID: 16474404, 20523244, 28911804). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces alanine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 246 of the BRAF protein (p.Ala246Pro).