Submissions for variant NM_002880.4(RAF1):c.768G>T (p.Arg256Ser)

dbSNP: rs397516826

Total submissions: 7

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen RASopathy Variant Curation Expert Panel	RCV000523940	SCV000616377	likely pathogenic	RASopathy	2024-12-03	reviewed by expert panel	curation	The c.768G>T variant in the RAF1 gene is a missense variant predicted to cause substitution of arginine by serine at amino acid 256 (p.Arg256Ser). This variant is absent from gnomAD v2 (PM2_Supporting). The computational predictor REVEL gives a score of 0.665, which does not meet PP3 or BP4. This variant is located in the CR2 critical functional domain as defined by the ClinGen RASopathy Expert Panel (PM1). This variant has been reported in 3 individuals with clinical features of Noonan syndrome (PS4_Moderate, PMIDs: 17603483, 22190897, 31292302). In vitro functional studies provide some evidence that the p.Arg256Ser variant may impact protein function (PMID: 20679480). ERK phosphorylation assay showed that the p.Arg256Ser variant led to significantly increased phosphorylation compared to wild-type (PS3_Supporting; PMID:20679480). In summary, this variant meets criteria to be classified as likely pathogenic for autosomal dominant RASopathies based on ACMG/AMP criteria applied, as specified by the ClinGen RASopathy Variant Curation Expert Panel: PS4_Moderate, PM1, PS3_Supporting, PM2_Supporting (Specification Version 2.3, 12/3/2024)
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000037701	SCV000061363	pathogenic	Noonan syndrome	2007-09-19	criteria provided, single submitter	clinical testing
GeneDx	RCV000159072	SCV000209014	pathogenic	not provided	2024-05-03	criteria provided, single submitter	clinical testing	Published functional studies demonstrate a damaging effect on protein localization and activity (PMID: 20679480); Not observed in large population cohorts (gnomAD); The majority of missense variants in this gene are considered pathogenic (HGMD); 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, 37777071, 24957944, 9689060, 15520807, 17603483, 29493581, 19020799, 20679480)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000523940	SCV002548259	pathogenic	RASopathy	2022-05-02	criteria provided, single submitter	clinical testing	Variant summary: RAF1 c.768G>T (p.Arg256Ser) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251458 control chromosomes (gnomAD). c.768G>T has been reported in the literature in individuals affected with Noonan Syndrome (Pandit_2007, Digilio_2011, Shoji_2019). These data indicate that the variant is likely to be associated with disease. Experimental evidence evaluating an impact on protein function demonstrated the catalytic activity of the variant was significantly increased compared to wild-type, binding of 14-3-3 proteins to C-RAF was impaired and subcellular localization was altered (Molzan_2010). Two ClinVar submitters including an expert panel (ClinGen RASopathy Variant Curation Expert Panel) (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000523940	SCV003525044	pathogenic	RASopathy	2024-10-07	criteria provided, single submitter	clinical testing	This sequence change replaces arginine, which is basic and polar, with serine, which is neutral and polar, at codon 256 of the RAF1 protein (p.Arg256Ser). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with Noonan syndrome (PMID: 17603483; internal data). ClinVar contains an entry for this variant (Variation ID: 40599). Invitae Evidence Modeling incorporating data from in vitro experimental studies (internal data) indicates that this missense variant is expected to disrupt RAF1 function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects RAF1 function (PMID: 20679480). This variant disrupts the p.Arg256 amino acid residue in RAF1. Other variant(s) that disrupt this residue have been determined to be pathogenic (internal data). 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.
Ambry Genetics	RCV004018717	SCV004936057	pathogenic	Cardiovascular phenotype	2023-10-18	criteria provided, single submitter	clinical testing	The c.768G>T (p.R256S) alteration is located in exon 7 (coding exon 6) of the RAF1 gene. This alteration results from a G to T substitution at nucleotide position 768, causing the arginine (R) at amino acid position 256 to be replaced by a serine (S). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This variant has been reported as heterozygous in two other individuals with clinical features consistent with RAF1-related RASopathy (Pandit, 2007; Molzan, 2010). Three other alterations at the same codon, c.766A>G (p.R256G), c.767G>A (p.R256K), and c.767G>C (p.R256T) have been detected in affected individuals (Burstein, 2021; Ambry internal data). This amino acid position is highly conserved in available vertebrate species. This variant is located in the conserved region 2 (CR2). The in silico prediction for this alteration is inconclusive. Based on the available evidence, this alteration is classified as pathogenic.
3billion	RCV005252702	SCV005905921	pathogenic	Noonan syndrome 5	2023-12-19	criteria provided, single submitter	clinical testing	The variant is not observed in the gnomAD v2.1.1 dataset. Predicted Consequence/Location: The variant is located in a mutational hot spot and/or well-established functional domain in which established pathogenic variants have been reported (PMID: 29493581, PMID). Missense changes are a common disease-causing mechanism. Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 20679480). In silico tool predictions suggest damaging effect of the variant on gene or gene product [REVEL: 0.67 (>=0.6, sensitivity 0.68 and specificity 0.92); 3Cnet: 0.97 (>=0.6, sensitivity 0.72 and precision 0.9)]. Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000040599 /PMID: 17603483 /3billion dataset). A different missense change at the same codon (p.Arg256Gly) has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000044631 /PMID: 32746448). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.