3-12604182-A-G

Variant names:

• chr3-12604182-A-G
• rs397516830
• NM_002880.4:c.788T>C

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1 PM2 PM5 PP2 PP3 PP5_Very_Strong

The NM_002880.4(RAF1):​c.788T>C​(p.Val263Ala) 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 Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V263G) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 33)
• Consequence: RAF1 NM_002880.4 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:5
• Conservation: PhyloP100: 9.32

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]

ACMG classification

Verdict is Pathogenic. Variant got 16 ACMG points.

• PM1: In a compositionally_biased_region Polar residues (size 47) in uniprot entity RAF1_HUMAN there are 14 pathogenic changes around while only 0 benign (100%) 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 chr3-12604182-A-C is described in Lovd as [Pathogenic].
• PP2: Missense variant in the RAF1 gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 47 curated pathogenic missense variants (we use a threshold of 10). The gene has 39 curated benign missense variants. Gene score misZ: 2.4628 (below the threshold of 3.09). Trascript score misZ: 3.4185 (above the threshold of 3.09). GenCC associations: The gene is linked to Noonan syndrome 5, dilated cardiomyopathy 1NN, Noonan syndrome with multiple lentigines, Noonan syndrome, cardiofaciocutaneous syndrome, familial isolated dilated cardiomyopathy, LEOPARD syndrome 2, Costello syndrome.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.817
• PP5: Variant 3-12604182-A-G is Pathogenic according to our data. Variant chr3-12604182-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 40608.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAF1	NM_002880.4	c.788T>C	p.Val263Ala	missense_variant	Exon 7 of 17	ENST00000251849.9	NP_002871.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAF1	ENST00000251849.9	c.788T>C	p.Val263Ala	missense_variant	Exon 7 of 17	1	NM_002880.4	ENSP00000251849.4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

RASopathy Pathogenic:2

Mar 11, 2024

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: RAF1 c.788T>C (p.Val263Ala) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251466 control chromosomes (gnomAD). c.788T>C has been reported in the literature in an individual affected with Noonan Syndrome (Razzaque_2007). These data suggest the variant may be associated with disease. Several publications report experimental evidence evaluating an impact on protein function (Razzaque_2007, Molzan_2010, Dhandapany_2015). The variant exhibited increased kinase activity in comparison to the WT protein and results in the constitutive activatation of the ERK/MAPK pathway. Additionally, other variants affecting the same amino acid (p.Val263Gly and p.Val263Asp) have been reported in individuals with Noonan Syndrome and have been classified as pathogenic/likely pathogenic by our laboratory. The following publications have been ascertained in the context of this evaluation (PMID: 24777450, 20679480, 17603482). ClinVar contains an entry for this variant (Variation ID: 40608). Based on the evidence outlined above, the variant was classified as likely pathogenic. -

Oct 22, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces valine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 263 of the RAF1 protein (p.Val263Ala). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of RAF1-related conditions (PMID: 17603482; internal data). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 40608). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) 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, 20679480, 24777450). This variant disrupts the p.Val263 amino acid residue in RAF1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 22821648). 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. -

not provided Pathogenic:1

Nov 21, 2024

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Missense variants in this gene are a common cause of disease and they are underrepresented in the general population; This variant is associated with the following publications: (PMID: 24803665, 29271604, 20679480, 24777450, 22821648, 33300679, 17603482, 38205249, 24957944, 9689060, 15520807, 29493581, 19020799, 17603483) -

Cardiovascular phenotype Pathogenic:1

Jun 07, 2019

Ambry Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.V263A variant (also known as c.788T>C), located in coding exon 6 of the RAF1 gene, results from a T to C substitution at nucleotide position 788. The valine at codon 263 is replaced by alanine, an amino acid with similar properties, and occurs in the conserved region 2 domain. This variant has been detected in an individual reported to have Noonan syndrome with hypertrophic cardiomyopathy (Razzaque MA et al. Nat. Genet., 2007 Aug;39:1013-7). In vitro functional studies have indicated that this variant results in increased kinase activity, increased phosphorylation of downstream effectors, and increased activation of the MAPK pathway (Razzaque MA et al. Nat. Genet., 2007 Aug;39:1013-7; Molzan M et al. Mol. Cell. Biol., 2010 Oct;30:4698-711; Dhandapany PS et al. Nat. Genet., 2014 Jun;46:635-639). Another variant affecting this codon was reported to occur de novo in a case with hypoplastic left heart syndrome considered associated with Noonan syndrome (Schulz S et al. Prenat. Diagn., 2012 Oct;32:1016-8). 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 5 Pathogenic:1

Aug 01, 2022

Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ACMG classification criteria: PS4 moderated, PM2 moderated, PM6 moderated, PP2 supporting, PP3 supporting -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.39	D
BayesDel_noAF	Pathogenic	0.32
CADD	Uncertain	25
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.73	D;.;T
Eigen	Uncertain	0.55
Eigen_PC	Uncertain	0.54
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Uncertain	0.90	D;D;T
M_CAP	Uncertain	0.29	D
MetaRNN	Pathogenic	0.82	D;D;D
MetaSVM	Uncertain	0.17	D
MutationAssessor	Uncertain	2.2	M;M;.
PrimateAI	Uncertain	0.79	T
PROVEAN	Benign	-2.3	N;D;D
REVEL	Pathogenic	0.73
Sift	Uncertain	0.0010	D;D;D
Sift4G	Benign	0.061	T;T;D
Polyphen		0.57	P;.;.
Vest4		0.85
MutPred		0.65		Loss of stability (P = 0.0159);Loss of stability (P = 0.0159);.;
MVP		0.96
MPC		1.2
ClinPred		0.91	D
GERP RS		5.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.80
gMVP		0.68

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: rs397516830; hg19: chr3-12645681; COSMIC: COSV52580063; COSMIC: COSV52580063;