This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, a(n) neutral and non-polar amino acid, with valine, a(n) neutral and non-polar amino acid, at codon 464 of the BRAF protein (p.Gly464Val). This missense change has been observed in individuals with cardio‐facio‐cutaneous syndrome (PMID: 2102266, 18039235, 18413255). For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects BRAF function (PMID: 19376813, 23680146, 23907581, 25155755). 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: 40364).

The BRAF c.1391G>T; p.Gly464Val variant (rs121913348) is reported in the literature in individuals affected with cardio-facio-cutaneous syndrome (Rodriguez-Viciana 2008, Yoon 2007). This variant is reported in ClinVar (Variation ID: 40364), but is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. The glycine at codon 464 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Functional analyses of the variant protein show increased kinase activation consistent with a gain of function mechanism (Hollestelle 2007, Wan 2004). Based on available information, this variant is considered to be likely pathogenic. References: Hollestelle A et al. Phosphatidylinositol-3-OH kinase or RAS pathway mutations in human breast cancer cell lines. Mol Cancer Res. 2007 Feb;5(2):195-201. Rodriguez-Viciana P and Rauen KA. Biochemical characterization of novel germline BRAF and MEK mutations in cardio-facio-cutaneous syndrome. Methods Enzymol. 2008;438:277-89. Wan PT et al. Mechanism of activation of the RAF-ERK signaling pathway by oncogenic mutations of B-RAF. Cell. 2004 Mar 19;116(6):855-67. Yoon G et al. Neurological complications of cardio-facio-cutaneous syndrome. Dev Med Child Neurol. 2007 Dec;49(12):894-9.

Variant has Tier II (potential) clinical significance as a diagnostic inclusion criterion in ovarian Sertoli-Leydig cell tumor, based on the following evidence: 1) Documented in one or more cancer databases (e.g., St. Jude Pecan, COSMIC, CIViC, OncoKB). 2) Information in the literature supports potential biologic effect of variant (PMIDs: 12068308, 15150094, 23680146). 3) Assists in diagnosis alone or along with other biomarkers based on small studies or few case reports (Evidence Level D; PMIDs: 23833300, 15150094, 17314276).

Somatic BRAF variants have been identified in up to 3% of cases of lung adenocar cinoma (Davies 2002).

The variant is not observed in the gnomAD v2.1.1 dataset. The variant is located in a mutational hot spot and/or well-established functional domain in which established pathogenic variants have been reported. Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.94; 3Cnet: 3CNET). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000040364). Different missense changes at the same codon (p.Gly504Arg, p.Gly504Glu) have been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000013964, VCV000279992, VCV000372572). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0101 - Gain of function is a known mechanism of disease in this gene and is associated with cardiofaciocutaneous syndrome (MIM#115150), LEOPARD syndrome type 3 (MIM#613707), and Noonan syndrome (MIM#613706). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from glycine to valine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0601 - Variant is located in the well-established functional protein tyrosine and serine/threonine kinase domain (DECIPHER, PMID: 15488754 ). (SP) 0702 - Other variants comparable to the one identified in this case, p.(Gly464Arg), p.(Gly464Glu) and p.(Gly464Ala), have strong previous evidence for pathogenicity (Clinvar). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported in individuals with cardiofaciocutaneous syndrome (PMID 18039235, PMID: 18413255, Clinvar). (SP) 0905 - No published segregation evidence has been identified for this variant. (I) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Expression of this variant in a zebrafish model showed developmental defects (PMID: 19376813). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

Variant classified as Uncertain significance and reported on 09-14-2022 by Victorian Clinical Genetics Services. GenomeConnect-CFC International assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.