ClinVar Miner

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

dbSNP: rs397516826
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen RASopathy Variant Curation Expert Panel RCV000523940 SCV000616377 likely pathogenic RASopathy 2024-09-17 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 4 (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 2.1, 9/17/2024)
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.

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