ClinVar Miner

Submissions for variant NM_005633.3(SOS1):c.1654A>T (p.Arg552Trp) (rs137852814)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen RASopathy Variant Curation Expert Panel RCV000787999 SCV000927030 likely pathogenic Noonan syndrome and Noonan-related syndrome 2019-05-10 reviewed by expert panel curation The c.1654A>T (p.Arg552Trp) variant has been identified in 1 patient with clinical features of a RASopathy (PS4_Supporting; PMID: 22465605). This variant was absent from large population studies (PM2; gnomAD, http://gnomad.broadinstitute.org). Of note this p.Arg552 residue is defined as a hotspot by the RAS VCEP. This variant would have received PM5_Strong but the RAS EP decided that PM1 and PM5 cannot be used simultaneously and therefore the PM1 rule has been upgraded with expert judgement (PM1_Strong). Computational prediction tools and conservation analysis suggest that the p.Arg552Trp variant may impact the protein (PP3). The variant is located in the SOS1 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). 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): PS4_Supporting, PM2, PM1_Strong, PP2, PP3.
GeneDx RCV000414145 SCV000491038 pathogenic not provided 2015-08-03 criteria provided, single submitter clinical testing The R552W in the SOS1 gene has been reported in one family in association with pulmonary stenosis and Noonan syndrome (Ezquieta et al., 2012). Additionally, the R552W variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. R552W results in a non-conservative amino acid substitution at a position that is conserved across species. Several other missense variants have been reported in the same residue (R552G, R552T, G552K, R552M, R552S) suggesting this residue is a hotspot", and this residue has been shown to be structurally important (Lepri et al., 2011). Furthermore, missense variants in nearby residues (S548R, T549K, L550P) have been reported in the Human Gene Mutation Database in association with SOS1-related disorders (Stenson et al., 2014), further supporting the functional importance of this residue and this region of the protein.In summary, R552W in the SOS1 gene is interpreted as a disease-causing variant"
Blueprint Genetics RCV000414145 SCV000927585 likely pathogenic not provided 2018-03-09 criteria provided, single submitter clinical testing

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