chr3-12608823-T-C

Position:

• chr3-12608823-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 6P and 1B. PM1 PM2 PP2 PP5 BP4

The ENST00000251849.9(RAF1):​c.524A>G​(p.His175Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: RAF1 ENST00000251849.9 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:6 U:1
• Conservation: PhyloP100: 4.25

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 Uncertain_significance. Variant got 5 ACMG points.

• PM1: In a zinc_finger_region Phorbol-ester/DAG-type (size 46) in uniprot entity RAF1_HUMAN there are 5 pathogenic changes around while only 0 benign (100%) in ENST00000251849.9
• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), RAF1. . Gene score misZ 2.4628 (greater than the threshold 3.09). Trascript score misZ 3.4185 (greater than threshold 3.09). GenCC has associacion of gene with Noonan syndrome 5, dilated cardiomyopathy 1NN, Noonan syndrome with multiple lentigines, Noonan syndrome, cardiofaciocutaneous syndrome, familial isolated dilated cardiomyopathy, LEOPARD syndrome 2, Costello syndrome.
• PP5: Variant 3-12608823-T-C is Pathogenic according to our data. Variant chr3-12608823-T-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 40594.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=1, Pathogenic=4, Uncertain_significance=1}.
• BP4: Computational evidence support a benign effect (MetaRNN=0.28103697). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RAF1	NM_002880.4	c.524A>G	p.His175Arg	missense_variant	5/17	ENST00000251849.9	NP_002871.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RAF1	ENST00000251849.9	c.524A>G	p.His175Arg	missense_variant	5/17	1	NM_002880.4	ENSP00000251849	P3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:6 Uncertain:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Oct 16, 2023	Not observed in large population cohorts (gnomAD); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; The majority of missense variants in this gene are considered pathogenic (HGMD); This variant is associated with the following publications: (PMID: 33673806) -
Pathogenic, criteria provided, single submitter	clinical testing	Blueprint Genetics	Jan 12, 2018	- -

Noonan syndrome Pathogenic:2

Likely pathogenic, no assertion criteria provided	clinical testing	Service de Génétique Moléculaire, Hôpital Robert Debré	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	May 23, 2013	The His175Arg variant in the RAF1 gene has not been previously reported in the l iterature. This variant was not identified in either parent of this individual a nd therefore likely occurred de novo, assuming that non-medical explanations inc luding alternate paternity or undisclosed adoption have been ruled out. In addit ion, this variant has been found to segregate with clinical features consistent with Noonan syndrome in four individuals in one family tested by our laboratory. The His175Arg variant has not been identified in large, ethnically-distinct pop ulations by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS /). Computational analyses (biochemical amino acid properties, conservation, Ali gnGVGD, PolyPhen2, and SIFT) suggest this variant may not impact the protein, th ough this information is not predictive enough to rule out pathogenicity. In sum mary, this variant meets our criteria to be classified as pathogenic based on it s de novo occurrence (http://pcpgm.partners.org/LMM). -

Cardiovascular phenotype Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 14, 2023

The p.H175R variant (also known as c.524A>G), located in coding exon 4 of the RAF1 gene, results from an A to G substitution at nucleotide position 524. The histidine at codon 175 is replaced by arginine, an amino acid with highly similar properties. This variant has been reported to occur de novo in a case with features consistent with Noonan syndrome (NS), and has been reported to segregate with features consistent with NS in a family (external communication). This variant has also been detected in a cohort referred for hypertrophic cardiomyopathy genetic testing; however, details were limited (Hathaway J et al. BMC Cardiovasc Disord. 2021 Mar;21(1):126). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated 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

Pathogenic, criteria provided, single submitter

clinical testing

Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München

May 29, 2020

- -

RASopathy Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jul 26, 2022

Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This sequence change replaces histidine, which is basic and polar, with arginine, which is basic and polar, at codon 175 of the RAF1 protein (p.His175Arg). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with hypertrophic cardiomyopathy (PMID: 33673806). ClinVar contains an entry for this variant (Variation ID: 40594). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.78
BayesDel_addAF	Uncertain	0.079	D
BayesDel_noAF	Benign	-0.12
CADD	Uncertain	24
DANN	Benign	0.47
DEOGEN2	Uncertain	0.57	D;.;T
Eigen	Benign	-0.30
Eigen_PC	Benign	-0.037
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.91	D;D;D
M_CAP	Uncertain	0.096	D
MetaRNN	Benign	0.28	T;T;T
MetaSVM	Uncertain	-0.059	T
MutationAssessor	Benign	-1.3	N;N;.
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Pathogenic	0.87	D
PROVEAN	Benign	-1.0	N;N;N
REVEL	Uncertain	0.40
Sift	Benign	1.0	T;T;T
Sift4G	Benign	1.0	T;T;T
Polyphen		0.58	P;.;.
Vest4		0.42
MutPred		0.51		Loss of methylation at K179 (P = 0.0691);Loss of methylation at K179 (P = 0.0691);.;
MVP		0.71
MPC		0.73
ClinPred		0.59	D
GERP RS		5.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.36
gMVP		0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs397516822; hg19: chr3-12650322; COSMIC: COSV52580142; COSMIC: COSV52580142;