rs80338799

chr3-12585745-G-Achr3-12585745-G-C

Variant summary

Our verdict is Pathogenic. Variant got 17 ACMG points: 17P and 0B. PM1 PM2 PM5 PP2 PP3_Moderate PP5_Very_Strong

The NM_002880.4(RAF1):c.1472C>T(p.Thr491Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T491R) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: RAF1 NM_002880.4 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:6 O:1
• Conservation: PhyloP100: 10.0

Genes affected

RAF1 (HGNC:9829): (Raf-1 proto-oncogene, serine/threonine kinase) This gene is the cellular homolog of viral raf gene (v-raf). The encoded protein is a MAP kinase kinase kinase (MAP3K), which functions downstream of the Ras family of membrane associated GTPases to which it binds directly. Once activated, the cellular RAF1 protein can phosphorylate to activate the dual specificity protein kinases MEK1 and MEK2, which in turn phosphorylate to activate the serine/threonine specific protein kinases, ERK1 and ERK2. Activated ERKs are pleiotropic effectors of cell physiology and play an important role in the control of gene expression involved in the cell division cycle, apoptosis, cell differentiation and cell migration. Mutations in this gene are associated with Noonan syndrome 5 and LEOPARD syndrome 2. [provided by RefSeq, Jul 2008]

MKRN2 (HGNC:7113): (makorin ring finger protein 2) This gene encodes a probable E3 ubiquitin ligase containing several zinc finger domains, that is a member of the makorin RING zinc-finger protein family. This gene overlaps the v-raf-1 murine leukemia viral oncogene homolog 1 (RAF1) gene in an antisense orientation and may have a co-regulatory function with RAF1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]

ACMG classification

Verdict is Pathogenic. Variant got 17 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 9 uncertain in NM_002880.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr3-12585745-G-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 13959.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP2: Missense variant where missense usually causes diseases, RAF1
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.925
• PP5: Variant 3-12585745-G-A is Pathogenic according to our data. Variant chr3-12585745-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 21342.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-12585745-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RAF1	NM_002880.4	c.1472C>T	p.Thr491Ile	missense_variant	14/17	ENST00000251849.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RAF1	ENST00000251849.9	c.1472C>T	p.Thr491Ile	missense_variant	14/17	1	NM_002880.4	P3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:6 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

Noonan syndrome Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	May 28, 2013	The Thr491Ile has been identified in our laboratory in two probands with clinica l features of Noonan syndrome. In addition, this variant was not identified in t he parents of one proband in our laboratory, and therefore occurred de novo. Thi s variant has also been reported in the literature in one individual with clinic al features of Noonan syndrome and was not identified in 210 control individuals (Pandit 2007). Computational analyses (biochemical amino acid properties, conse rvation, AlignGVGD, and SIFT) suggest that the Thr491Ile variant may impact the protein. In summary, this variant meets our criteria to be classified as pathoge nic based on its de novo occurrence (http://pcpgm.partners.org/LMM). -
Likely pathogenic, no assertion criteria provided	literature only	Database of Curated Mutations (DoCM)	May 13, 2016	- -

RASopathy Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Invitae	May 12, 2022	For these reasons, this variant has been classified as Pathogenic. This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 491 of the RAF1 protein (p.Thr491Ile). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with Noonan syndrome (PMID: 17603483, 27753652, 30732632). ClinVar contains an entry for this variant (Variation ID: 21342). 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. Experimental studies have shown that this missense change affects RAF1 function (PMID: 17603483, 22826437). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. -
Pathogenic, reviewed by expert panel	curation	ClinGen RASopathy Variant Curation Expert Panel	Apr 03, 2017	The c.1472C>T (p.Thr491Ile) variant in RAF1 has been reported in the literature in at least one individual with clinical features of a RASopathy (PS4 not met; PMID 17603483). 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). Computational prediction tools and conservation analysis suggest that the p.Thr491Ile variant may impact the protein (PP3). In vitro functional studies provide some evidence that the p.Thr491Ile variant may impact protein function (PS3; 20679480). 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. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PP2, PP3, PM1, PM2, PS3. -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Sep 08, 2023

Observed in multiple unrelated patients with Noonan spectrum disorders tested at GeneDx, in the published literature, and in ClinVar, including apparently de novo in an affected patient (Pandit et al., 2007; ClinVar SCV000061338.4; ClinVar); about 80% of individuals with a RAF1 variant develop hypertrophic cardiomyopathy; Published functional studies demonstrate impaired MEK kinase expression and constitutive ERK activation (Pandit et al., 2007) and show the variant is located in the activation segment of the CR3 (conserved region 3), a critical functional domain; Not observed in large population cohorts (gnomAD); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; The majority of missense variants in this gene are considered pathogenic (HGMD); This variant is associated with the following publications: (PMID: 26214590, 27236105, 23093928, 24803665, 25907612, 25333451, 27753652, 30732632, 31219622, 34328347, 29493581, 17603483, 9689060, 15520807, 17603482, 19020799) -

Cardiovascular phenotype Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 06, 2016

The p.T491I variant (also known as c.1472C>T), located in coding exon 13 of the RAF1 gene, results from a C to T substitution at nucleotide position 1472. The threonine at codon 491 is replaced by isoleucine, an amino acid with similar properties. This alteration has been reported in the literature in an individual with Noonan syndrome (Pandit B et al. Nat. Genet. 2007 Aug; 39(8):1007-12). Phosphorylation of the threonine at codon 491 has been shown to be important for the regulation of RAF1 activity, and the p.T491I variant has been shown to alter RAF1 function (Pandit B et al. Nat. Genet. 2007 Aug; 39(8):1007-12; Wu X et al. Mol. Cell. Biol. 2012 Oct; 32(19):3872-90). This variant was previously reported in the SNPDatabase as rs80338799. This variant was not reported in population-based cohorts in the following databases: NHLBI Exome Sequencing Project (ESP) and 1000 Genomes Project. In the ESP, this variant was not observed in 6503 samples (13006 alleles) with coverage at this position. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Noonan syndrome with multiple lentigines Other:1

not provided, no classification provided

literature only

GeneReviews

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.42	D
BayesDel_noAF	Pathogenic	0.37
Cadd	Pathogenic	32
Dann	Uncertain	1.0
DEOGEN2	Pathogenic	0.92	D;.;D
Eigen	Pathogenic	0.77
Eigen_PC	Pathogenic	0.80
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.97	D;D;D
M_CAP	Uncertain	0.18	D
MetaRNN	Pathogenic	0.92	D;D;D
MetaSVM	Uncertain	0.30	D
MutationAssessor	Benign	1.1	L;.;.
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Pathogenic	0.87	D
PROVEAN	Pathogenic	-5.4	D;D;D
REVEL	Pathogenic	0.86
Sift	Pathogenic	0.0	D;D;D
Sift4G	Uncertain	0.0060	D;D;D
Polyphen		0.99	D;.;.
Vest4		0.98
MutPred		0.80		Gain of methylation at K493 (P = 0.0498);.;.;
MVP		0.98
MPC		2.5
ClinPred		1.0	D
GERP RS		5.3
Varity_R		0.95
gMVP		0.78

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs80338799; hg19: chr3-12627244; COSMIC: COSV50104312; COSMIC: COSV50104312;