Submissions for variant NM_002880.4(RAF1):c.779C>T (p.Thr260Ile)

dbSNP: rs869025501

Total submissions: 6

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen RASopathy Variant Curation Expert Panel	RCV000696020	SCV001335315	uncertain significance	RASopathy	2020-03-09	reviewed by expert panel	curation	The c.779C>T (p.Thr260Ile) variant in RAF1 was absent from large population databases (PM2; gnomad.broadinstitute.org). It occurs in the CR2 domain of the protein, which has been identified as a region important for protein function (PM1, 29493581). In vitro functional assays indicate that this variant may impact protein function (PS3; PMID: 20679480). The variant is located in the RAF1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic variants are common (PP2; PMID: 29493581). Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. This variant has been observed in multiple probands who lacked consistent RASopathy phenotypes; however, many probands presented with cardiomyopathy (PMID: 17603483; Blueprint Genetics internal data, SCV000264163.2; Invitae internal data, SCV000824563.1; Ambry internal data, SCV000740058.2; GeneDx internal data, SCV000582743.4). Although criteria suggest that this variant is likely pathogenic given its location and in vitro functional studies, the lack of clear clinical presentations of a RASopathy phenotype supports that this variant is of uncertain significance at this time. RASopathy-specific ACMG/AMP criteria applied: PS3, PM1, PM2, PP2.
Blueprint Genetics	RCV000208050	SCV000264163	likely pathogenic	Primary familial hypertrophic cardiomyopathy	2015-02-03	criteria provided, single submitter	clinical testing
GeneDx	RCV000494156	SCV000582743	pathogenic	not provided	2023-07-31	criteria provided, single submitter	clinical testing	Not observed at significant frequency in large population cohorts (gnomAD); Missense variants in this gene are often considered pathogenic (HGMD); Published functional studies suggest a damaging effect as the p.(T260I) variant has decreased affinity for C-RAF-PSer, increased enzymatic activity and decreases p.S259 phosphorylation suggestive of an overactive Ras-RAF-MAPK pathway (Molzan et al., 2010); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 24803665, 33686258, 17603483, 33673806, 29493581, 24957944, 9689060, 15520807, 17603482, 19020799, 20679480)
Ambry Genetics	RCV000617372	SCV000740058	likely pathogenic	Cardiovascular phenotype	2016-10-31	criteria provided, single submitter	clinical testing	The p.T260I variant (also known as c.779C>T), located in coding exon 6 of the RAF1 gene, results from a C to T substitution at nucleotide position 779. The threonine at codon 260 is replaced by isoleucine, an amino acid with similar properties. This alteration is located in the consensus recognition site for 14-3-3, which is a hotspot for Noonan syndrome (NS) mutations. Mutations in this region have been associated with a high prevalence of hypertrophic cardiomyopathy (HCM), and this variant has been previously reported in an HCM cohort (Pandit B et al. Nat. Genet. 2007;39:1007-12). Functional studies have demonstrated that this alteration leads to decreased phosphorylation of an invariant phosphorylated serine in the 14-3-3 recognition site, impaired 14-3-3 binding affinity, and increased RAF1 catalytic activity (Molzan M et al. Mol. Cell. Biol. 2010;30:4698-711). Furthermore, a likely pathogenic alteration affecting the same codon (p.T260R) has been reported in an individual with NS (Pandit B et al. Nat. Genet. 2007;39:1007-12). 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.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000696020	SCV000824563	pathogenic	RASopathy	2022-10-17	criteria provided, single submitter	clinical testing	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 RAF1 protein function. This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 260 of the RAF1 protein (p.Thr260Ile). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of Noonan syndrome (PMID: 17603483; Invitae). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 222774). Experimental studies have shown that this missense change affects RAF1 function (PMID: 20679480). This variant disrupts the p.Thr260 amino acid residue in RAF1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 17603483; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
Revvity Omics, Revvity	RCV000494156	SCV002019014	likely pathogenic	not provided	2019-11-27	criteria provided, single submitter	clinical testing