ClinVar Miner

Submissions for variant NM_002880.4(RAF1):c.775T>A (p.Ser259Thr)

dbSNP: rs3730271
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen RASopathy Variant Curation Expert Panel RCV000522675 SCV000616422 pathogenic RASopathy 2017-04-03 reviewed by expert panel curation The c.775T>A (p.Ser259Thr) variant in RAF1 has been reported in the literature in at least 2 unconfirmed de novo occurrences in patients with clinical features of a RASopathy (PM6_Strong; APHP-Robert Debré Hospital internal data; GTR ID's: 28338). The p.Ser259Thr variant has been identified in at least 8 independent occurrences in patients with a RASopathy (PS4_Supporting; GeneDx, Partners LMM, Institute of Human Genetics, Otto von Guericke University Magdeburg internal data; GTR ID's: 26957, 21766, 506381 PMID: 21784453; ClinVar SCV000061360.5; SCV000209017.10). The p.Ser259Thr variant in RAF1 has been reported to segregate with clinical features of a RASopathy in at least 3 family members (PP1; GeneDx, Institute of Human Genetics, Otto von Guericke University Magdeburg internal data; GTR ID's: 26957, 506381; ClinVar SCV000209017.9). In vitro functional studies provide some evidence that the p.Ser259Thr variant may impact protein function (PS3; PMID: 21784453, 20052757). At least 2 other pathogenic missense variants have been previously identified at this codon of RAF1 which may indicate that this residue is critical to the function of the protein (PM5_Strong; ClinVar 40603, 40602, 228288). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of RAF1 (PM1; PMID 29493581). 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 missense variants are common (PP2; PMID: 29493581). Computational prediction tools and conservation analysis suggest that the p.Ser259Thr 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): PM6_Strong, PS4_Supporting, PP1, PM5_Strong, PM2, PM1, PP2, PP3, PS3.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000037698 SCV000061360 likely pathogenic Noonan syndrome 2010-09-09 criteria provided, single submitter clinical testing The Ser259Thr variant in RAF1 has been previously identified in two individuals with clinical features of Noonan syndrome (Ko 2008, LMM unpublished data). In ad dition, two different amino acid changes at this location (Ser259Phe, Ser259Tyr) have been identified in individuals with Noonan spectrum features, suggesting a lterations at this amino acid are not tolerated (Pandit 2007, Kobayashi 2009; LM M unpublished data). Ser259 is also known to be of critical importance to the r egulation of the RAF1 protein (Kobayashi 2009). Therefore, it is likely that thi s variant is pathogenic.
GeneDx RCV000159074 SCV000209017 pathogenic not provided 2023-03-16 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); Published functional studies demonstrate increased activation of MEK and ERK (Kobayashi et al., 2010; Lee et al., 2011); Missense variants in this gene are often considered pathogenic (HGMD); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 20052757, 24957944, 9689060, 15520807, 17603483, 17603482, 29493581, 19020799, 33318624, 21784453)
Labcorp Genetics (formerly Invitae), Labcorp RCV000522675 SCV001379118 pathogenic RASopathy 2022-11-19 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Ser259 amino acid residue in RAF1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 17603483, 20052757, 21784453). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Experimental studies have shown that this missense change affects RAF1 function (PMID: 21784453). 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. ClinVar contains an entry for this variant (Variation ID: 40601). This missense change has been observed in individuals with Noonan syndrome (PMID: 19020799; Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with threonine, which is neutral and polar, at codon 259 of the RAF1 protein (p.Ser259Thr).
Mayo Clinic Laboratories, Mayo Clinic RCV000159074 SCV001714081 pathogenic not provided 2019-06-23 criteria provided, single submitter clinical testing PM6_Strong, PS3, PS4_Supporting, PM1, PM2, PM5_Strong, PP2, PP3, PP1
Genetics and Molecular Pathology, SA Pathology RCV000037698 SCV002761577 pathogenic Noonan syndrome 2022-06-21 criteria provided, single submitter clinical testing The RAF1 c.775T>A variant is classified as a Pathogenic variant (PS4, PS3, PM5, PP3) This variant is a single nucleotide change in exon 7/18 of the RAF1 gene, which is predicted to change the amino acid serine at position 259 in the protein to threonine. The variant has been reported multiple times in patients with Noonan syndrome and with clinical features of a RASopathy (PMID: 19020799, 21784453, 33318624, 29493581). This variant is in dbSNP (rs3730271) but is absent from population databases (PS4). Functional studies have shown that this variant may impact protein function by increasing activation of MEK and ERK (PMID: 21784453) (PS3). Missense variants in the same residue (p.S259C, p.S259F, p.S259P, p.A259Y) have been previously reported as pathogenic in association with Noonan spectrum disorders (PM5).The variant has been reported in the ClinVar and HGMD as pathogenic/ disease causing. Computational predictions support a deleterious effect on the gene or gene product (PP3).
Revvity Omics, Revvity RCV000159074 SCV003819033 pathogenic not provided 2022-01-10 criteria provided, single submitter clinical testing
Molecular Genetics, Centre for Human Genetics RCV003450656 SCV004190087 pathogenic Noonan syndrome 1 no assertion criteria provided clinical testing

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