Submissions for variant NM_002880.4(RAF1):c.770C>T (p.Ser257Leu)

dbSNP: rs80338796

Total submissions: 43

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen RASopathy Variant Curation Expert Panel	RCV000157426	SCV000616378	pathogenic	Noonan syndrome	2017-04-03	reviewed by expert panel	curation	The c.770C>T (p.Ser257Leu) 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; PMID 17603482,22389993, 23877478, 23312806, 25706034). In vitro functional studies provide some evidence that the p.Ser257Leu variant may impact protein function (PS3; PMID 17603482). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). 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). 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). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. ACMG/AMP criteria applied: PP2, PM1, PM2, PS3, PM6_Strong.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000824754	SCV000200043	pathogenic	Noonan syndrome with multiple lentigines; Noonan syndrome	2013-05-23	criteria provided, single submitter	clinical testing	The p.Ser257Leu variant has been associated with the clinical features of RASopa thy disorders (Razzaque 2007, Pandit 2007). This variant has been reported to ha ve occurred de novo in sporadic cases. Individuals with pathogenic variants in exon 7 or 17 in RAF1 have a high incidence of hypertrophic cardiomyopathy (80-95 %, Razzaque 2007, Pandit 2007). In summary, this variant meets criteria to be cl assified as pathogenic for RASopathy disorders in an autosomal dominant manner b ased upon published literature and de novo occurrence in affected individuals.
Blueprint Genetics	RCV000157426	SCV000207169	pathogenic	Noonan syndrome	2015-10-05	criteria provided, single submitter	clinical testing
GeneDx	RCV000157685	SCV000209016	pathogenic	not provided	2022-09-09	criteria provided, single submitter	clinical testing	Published functional studies demonstrate that S257L produces a gain of function effect with higher kinase activity than wild-type protein (Razzaque et al., 2007; Lee et al., 2011); 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: 26918529, 23877478, 30384889, 35050212, 32506814, 31219622, 34184824, 30417923, 25706034, 24033266, 23312806, 22389993, 17603483, 20052757, 24775816, 24803665, 28973083, 29084544, 28777121, 30732632, 30138938, 30055033, 30355600, 30105547, 21784453, 21440552, 28991257, 30050098, 29907801, 31395954, 31560489, 31324109, 31163979, 32573669, 32668055, 34136434, 33318624, 17603482, 32981126, 33673806, 32410215, 33240318, 32746448, 32368696, 34006472, 24957944, 9689060, 15520807, 29493581)
Molecular Diagnostics Lab, Nemours Children's Health, Delaware	RCV000157685	SCV000263046	pathogenic	not provided	2015-07-21	criteria provided, single submitter	clinical testing
Invitae	RCV000149826	SCV000287743	pathogenic	RASopathy	2023-12-24	criteria provided, single submitter	clinical testing	This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 257 of the RAF1 protein (p.Ser257Leu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with Noonan syndrome, both with and without multiple lentigines (PMID: 17603482, 17603483, 20052757, 22389993, 23877478). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 13957). 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 with a positive predictive value of 95%. Experimental studies have shown that this missense change affects RAF1 function (PMID: 17603482, 20052757). For these reasons, this variant has been classified as Pathogenic.
Eurofins Ntd Llc (ga)	RCV000157685	SCV000341105	pathogenic	not provided	2016-04-14	criteria provided, single submitter	clinical testing
Fulgent Genetics, Fulgent Genetics	RCV000515222	SCV000611310	pathogenic	LEOPARD syndrome 2; Noonan syndrome 5; Dilated cardiomyopathy 1NN	2021-07-01	criteria provided, single submitter	clinical testing
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München	RCV000014985	SCV000680354	pathogenic	Noonan syndrome 5	2017-11-15	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000149826	SCV000918146	pathogenic	RASopathy	2018-12-11	criteria provided, single submitter	clinical testing	Variant summary: RAF1 c.770C>T (p.Ser257Leu) results in a non-conservative amino acid change located in the CR2 domain of the encoded protein sequence that is involved in regulatory phosphorylation and association with the 14-3-3 protein (Razzaque 2007, Pandit 2007). Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 246848 control chromosomes (gnomAD). c.770C>T has been reported in the literature in multiple individuals affected with Noonan Syndrome and Related Conditions, where several of these individuals also had hypertrophic cardiomyopathy or other cardiac manifestations (e.g. Razzaque 2007, Pandit 2007, Denayer 2010, Alfieri 2008, Croonen 2013, Zarare 2013, Lee 2011, Xu 2017). The variant has also been reported in some patients with LEOPARD syndrome (see e.g. Pandit 2007, Carcavilla 2013, Xu 2017). In all confirmed cases the variant occurred in heterozygous state as a de novo mutation (see e.g. Pandit 2007, Denayer 2010, Croonen 2013, Zarare 2013, Xu 2017). These data indicate that the variant is very likely to be associated with disease. Several publications reported experimental evidence evaluating an impact on protein function, demonstrating increased kinase activity (Razzaque 2007), increased activation of MEK and ERK (Lee 2011) and altered signaling in cardiomyocytes consistent with that observed in cardiac hypertrophy (Dhandapany 2011). 11 clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic (10x) / likely pathogenic (1x). Based on the evidence outlined above, the variant was classified as pathogenic.
Agnes Ginges Centre for Molecular Cardiology, Centenary Institute	RCV000157426	SCV000996383	pathogenic	Noonan syndrome	2017-11-16	criteria provided, single submitter	research	The RAF1 Ser257Leu variant has been previously reported in multiple Noonan syndrome cases (see literature), including at least 6 cases where the variant was found to arise de novo (Zarate YA, et al., 2013; Kobayashi T, et al., 2010; Pandit B, et al., 2007). We identified this variant in a young male patient diagnosed with Noonan syndrome. RAF1 Ser257Leu is absent in the Exome Aggregation Consortium dataset (http://exac.broadinstitute.org/), as well as the Genome Aggregation Database (http://gnomad.broadinstitute.org/). In silico tools SIFT and MutationTaster predict this variant to be deleterious, however PolyPhen-2 predicts this variant to be "benign". In summary, based on rarity in the general population, presence in multiple Noonan syndrome patients, the high rate of de novo occurrences and because the variant is located in a functional 'hotspot' we classify the RAF1 Ser257Leu as "pathogenic".
Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn	RCV000856803	SCV000999369	pathogenic	Noonan syndrome 1		criteria provided, single submitter	clinical testing
Centre for Mendelian Genomics, University Medical Centre Ljubljana	RCV000014986	SCV001369226	pathogenic	LEOPARD syndrome 2	2019-05-20	criteria provided, single submitter	clinical testing	This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PS3,PM1,PM2,PM5,PP2,PP3.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000157685	SCV001473076	pathogenic	not provided	2020-06-05	criteria provided, single submitter	clinical testing	The RAF1 c.770C>T; p.Ser257Leu variant (rs80338796) has been reported in multiple individuals diagnosed with Noonan syndrome (Razzaque 2007, Pandit 2007, Kobayashi 2010, Zarate 2014, Hopper 2015) or LEOPARD syndrome (Pandit 2007, Carcavilla 2013). The variant is reported as pathogenic in ClinVar by multiple sources (Variation ID: 13957) absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. This variant is located in a region critical for the phosphorylation of serine-259 and its association with 14-3-3, which is involved in the negative regulation of RAF1 activity (Razzaque 2007, Kobayashi 2010). Functional characterization of the p.Ser257Leu variant protein indicates a loss of serine-259 phosphorylation and reduced association with 14-3-3 (Kobayashi 2010). This leads to an over-activation of MEK and ERK signaling (Razzaque 2007, Kobayashi 2010), consistent with the established disease mechanisms of Noonan Syndrome. Based on available information, this variant is considered to be pathogenic. References: Carcavilla A et al. LEOPARD syndrome: a variant of Noonan syndrome strongly associated with hypertrophic cardiomyopathy. Rev Esp Cardiol (Engl Ed). 2013 May;66(5):350-6. Hopper R et al. Neonatal pulmonary arterial hypertension and Noonan syndrome: two fatal cases with a specific RAF1 mutation. Am J Med Genet A. 2015 Apr;167A(4):882-5. Kobayashi T et al. Molecular and clinical analysis of RAF1 in Noonan syndrome and related disorders: dephosphorylation of serine 259 as the essential mechanism for mutant activation. Hum Mutat. 2010 Mar;31(3):284-94. Pandit B et al. Gain-of-function RAF1 mutations cause Noonan and LEOPARD syndromes with hypertrophic cardiomyopathy. Nat Genet. 2007 Aug;39(8):1007-12. Razzaque M et al Germline gain-of-function mutations in RAF1 cause Noonan syndrome. Nat Genet. 2007 Aug;39(8):1013-7 Zarate Y et al. Unique cerebrovascular anomalies in Noonan syndrome with RAF1 mutation. J Child Neurol. 2014 Aug;29(8):NP13-7.
Mayo Clinic Laboratories, Mayo Clinic	RCV000157685	SCV001714082	pathogenic	not provided	2022-06-15	criteria provided, single submitter	clinical testing	PP2, PM1, PM2, PS2_very_strong, PS3, PS4
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	RCV001731288	SCV001984841	pathogenic	RAF1-related disorder	2020-10-21	criteria provided, single submitter	clinical testing	This variant has been previously reported as a de novo change in patients with Noonan Syndrome (PMID: 17603482, 23877478) and LEOPARD syndrome 2 (PMID: 22389993, 24775816). This variant has been classified as Pathogenic by the ClinGen Rasopathy Expert Panel. Functional studies indicate that the p.Ser257Leu produces a gain-of-function effect with higher kinase activity than wild-type protein (PMID: 17603482). It is absent from the gnomAD population database and thus is presumed to be rare. In silico tools used to predict the effect of this variant on protein function yield discordant results. Analysis of the parental samples was negative for the variant, indicating this variant likely occurred as a de novo event. Based on the available evidence, the c.770C>T (p.Ser257Leu) variant is classified as Pathogenic.
Centogene AG - the Rare Disease Company	RCV000014985	SCV002059455	pathogenic	Noonan syndrome 5	2020-02-11	criteria provided, single submitter	clinical testing
Genome Diagnostics Laboratory, The Hospital for Sick Children	RCV001813205	SCV002060975	pathogenic	Noonan syndrome and Noonan-related syndrome	2021-04-26	criteria provided, single submitter	clinical testing
Centro Nacional de Genética Medica "Dr. Eduardo E. Castilla", Administración Nacional de Laboratorios e Institutos de Salud	RCV000157685	SCV002098092	pathogenic	not provided	2022-02-02	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000157685	SCV002496785	pathogenic	not provided	2022-12-01	criteria provided, single submitter	clinical testing	RAF1: PS2:Very Strong, PM2, PS3:Supporting
3billion	RCV000014985	SCV002521319	pathogenic	Noonan syndrome 5	2022-05-22	criteria provided, single submitter	clinical testing	The variant is not observed in the gnomAD v2.1.1 dataset. The missense variant is located in a mutational hot spot and/or well-established functional domain in which established pathogenic variants have been reported. 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: 17603482, 20052757). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.65; 3Cnet: 0.08). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000013957). The variant has been previously reported as de novo in at least two similarly affected unrelated individuals (PMID: 17603483, 23877478) and as assumed (i.e. paternity and maternity not confirmed) de novo in at least two similarly affected unrelated individuals (PMID: 17603482, 22389993, 23877478, 25706034). Different missense changes at the same codon (p.Ser257Pro, p.Ser257Thr) have been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000040600, VCV000618340). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.
Ambry Genetics	RCV002399323	SCV002669882	pathogenic	Cardiovascular phenotype	2021-08-04	criteria provided, single submitter	clinical testing	The p.S257L pathogenic mutation (also known as c.770C>T), located in coding exon 6 of the RAF1 gene, results from a C to T substitution at nucleotide position 770. The serine at codon 257 is replaced by leucine, an amino acid with dissimilar properties. This alteration has been reported in numerous individuals with a diagnosis of Noonan syndrome or LEOPARD syndrome, including as a de novo alteration in two individuals in which paternity was confirmed (Pandit B et al. Nat Genet, 2007 Aug;39:1007-12; Razzaque MA et al. Nat Genet, 2007 Aug;39:1013-7; Kobayashi T et al. Hum Mutat, 2010 Mar;31:284-94; Carcavilla A et al. Rev Esp Cardiol (Engl Ed), 2013 May;66:350-6; Xu S et al. BMC Med Genomics, 2017 10;10:62; Vasilescu C et al. J Am Coll Cardiol, 2018 11;72:2324-2338; Chinton J et al. Arch Argent Pediatr, 2019 10;117:330-337). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	RCV000014985	SCV002767731	pathogenic	Noonan syndrome 5	2020-10-19	criteria provided, single submitter	clinical testing	A heterozygous missense variant was identified, NM_002880.3(RAF1):c.770C>T in exon 7 of the RAF1 gene. This substitution is predicted to create a major amino acid change from a serine to a leucine at position 257 of the protein; NP_002871.1(RAF1):p.(Ser257Leu). The serine at this position has very high conservation (100 vertebrates, UCSC), and is not situated in a known functional domain (NCBI, PDB). In silico software predictions of the pathogenicity of this variant are conflicting (FATHMM, PolyPhen2, MutationAssessor, PROVEAN). The variant is not present in the gnomAD population database. It is located within a mutational hotspot and has been previously reported as pathogenic in patients with Noonan syndrome (ClinGen RASopathy Variant Curation Expert Panel). Analysis of parental samples indicated that this variant is de novo. Based on information available at the time of curation, this variant has been classified as PATHOGENIC.
Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province	RCV000014985	SCV003915615	pathogenic	Noonan syndrome 5	2022-03-22	criteria provided, single submitter	clinical testing
Institute of Human Genetics, University Hospital Muenster	RCV003231105	SCV003929505	pathogenic	See cases	2023-04-04	criteria provided, single submitter	clinical testing	ACMG categories: PS3,PM1,PM2,PP3,PP5
Neuberg Centre For Genomic Medicine, NCGM	RCV000014985	SCV004047601	pathogenic	Noonan syndrome 5		criteria provided, single submitter	clinical testing	The missense variant c.770C>T (p.Ser257Leu) in RAF1 gene has been reported in heterozygous state in many individuals affected with Noonan syndrome, both with and without multiple lentigines (Kobayashi T et al., 2010). Experimental studies have shown that this missense change leads to increased activation of MEK, ERK, and ELK in vitro (Razzaque et al., 2007). The p.Ser257Leu variant is novel (not in any individuals) in gnomAD Exomes and 1000 Genomes. This variant has been reported to the ClinVar database as Pathogenic. The amino acid Ser at position 257 is changed to a Leu changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Ser257Leu in RAF1 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The variant is predicted to be probably damaging by PolyPhen 2 and deleterious by SIFT. For these reasons, this variant has been classified as Pathogenic.
OMIM	RCV000014985	SCV000035241	pathogenic	Noonan syndrome 5	2007-08-01	no assertion criteria provided	literature only
OMIM	RCV000014986	SCV000035242	pathogenic	LEOPARD syndrome 2	2007-08-01	no assertion criteria provided	literature only
GeneReviews	RCV000020509	SCV000040960	not provided	Noonan syndrome with multiple lentigines		no assertion provided	literature only
Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP)	RCV000014985	SCV000143821	not provided	Noonan syndrome 5		no assertion provided	not provided
Baylor Genetics	RCV000149826	SCV000196668	pathogenic	RASopathy		no assertion criteria provided	clinical testing	Variant classified using ACMG guidelines
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	RCV000157685	SCV000207668	pathogenic	not provided	2015-01-15	no assertion criteria provided	clinical testing
Database of Curated Mutations (DoCM)	RCV000157426	SCV000507276	likely pathogenic	Noonan syndrome	2016-05-13	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000436233	SCV000507277	likely pathogenic	Neoplasm of the large intestine	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000418940	SCV000507278	likely pathogenic	Lung adenocarcinoma	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000428775	SCV000507279	likely pathogenic	Gastric adenocarcinoma	2016-05-31	no assertion criteria provided	literature only
Database of Curated Mutations (DoCM)	RCV000435984	SCV000507280	likely pathogenic	Malignant melanoma of skin	2016-05-31	no assertion criteria provided	literature only
Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital	RCV000014985	SCV001482333	pathogenic	Noonan syndrome 5	2019-05-31	no assertion criteria provided	research
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000157685	SCV001743956	pathogenic	not provided		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000157685	SCV001956376	pathogenic	not provided		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000157685	SCV001974063	pathogenic	not provided		no assertion criteria provided	clinical testing
Division of Human Genetics, National Health Laboratory Service/University of the Witwatersrand	RCV000856803	SCV003840161	pathogenic	Noonan syndrome 1		no assertion criteria provided	research
Molecular Genetics, Centre for Human Genetics	RCV000856803	SCV004190086	pathogenic	Noonan syndrome 1		no assertion criteria provided	clinical testing