7-140801537-T-A

Position:

• chr7-140801537-T-A

Variant summary

Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PS4_Supporting PM6 PM2 PS1 PP3 PP2 PM1

This summary comes from the ClinGen Evidence Repository: The c.735A>T p.Leu245Phe variant in BRAF has been identified in at least 2 independent occurrences, one of which was de novo, in patients with clinical features of a RASopathy (PM6, PS4_Supporting; Partners LMM, University Magdeburg internal data; GTR Lab IDs: 21766, 506381 PMID:19206169, 22190897). This variant was absent from large population studies (PM2; gnomAD, http://gnomad.broadinstitute.org). Computational prediction tools and conservation analysis suggest that the p.Leu245Phe variant may impact the protein (PP3). The variant is located in the BRAF 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). Of note, the p.Leu245Phe change has also been reported as a consequence of the c.735A>C variant in BRAF, which has been classified as pathogenic and therefore supports that this residue may be critical to protein function (PS1; ClinVar ID: 40347). 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 BRAF (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): PS4_Supporting, PM6, PM1, PM2, PS1, PP2, PP3. LINK:https://erepo.genome.network/evrepo/ui/classification/CA280029/MONDO:0021060/004

• Frequency: Genomes: not found (cov: 32)
• Consequence: BRAF NM_004333.6 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:5 O:1
• Conservation: PhyloP100: 3.38

Genes affected

BRAF (HGNC:1097): (B-Raf proto-oncogene, serine/threonine kinase) This gene encodes a protein belonging to the RAF family of serine/threonine protein kinases. This protein plays a role in regulating the MAP kinase/ERK signaling pathway, which affects cell division, differentiation, and secretion. Mutations in this gene, most commonly the V600E mutation, are the most frequently identified cancer-causing mutations in melanoma, and have been identified in various other cancers as well, including non-Hodgkin lymphoma, colorectal cancer, thyroid carcinoma, non-small cell lung carcinoma, hairy cell leukemia and adenocarcinoma of lung. Mutations in this gene are also associated with cardiofaciocutaneous, Noonan, and Costello syndromes, which exhibit overlapping phenotypes. A pseudogene of this gene has been identified on the X chromosome. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Pathogenic. Variant got 13 ACMG points.

• PS1: For more information check the summary or visit ClinGen Evidence Repository.
• PS4: For more information check the summary or visit ClinGen Evidence Repository.
• PM1: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PM6: For more information check the summary or visit ClinGen Evidence Repository.
• PP2: For more information check the summary or visit ClinGen Evidence Repository.
• PP3: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRAF	NM_001374258.1	c.735A>T	p.Leu245Phe	missense_variant	6/20	ENST00000644969.2	NP_001361187.1
BRAF	NM_004333.6	c.735A>T	p.Leu245Phe	missense_variant	6/18	ENST00000646891.2	NP_004324.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRAF	ENST00000644969.2	c.735A>T	p.Leu245Phe	missense_variant	6/20		NM_001374258.1	ENSP00000496776
BRAF	ENST00000646891.2	c.735A>T	p.Leu245Phe	missense_variant	6/18		NM_004333.6	ENSP00000493543	P4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:5 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

Neurodevelopmental delay Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille

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Cardio-facio-cutaneous syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Aug 22, 2012

The Leu245Phe variant in BRAF has been previously identified in the literature i n two patients, one with clinical features of Cardio-Facio-Cutaneous Syndrome an d one with clinical features of Leopard Syndrome, and was shown to be absent fro m 600 control chromosomes (Sarkozy 2009, Koudova 2009). This variant has been pr eviously identified by our laboratory in a single patient with clinical features of Noonan Syndrome but the nucleotide change differs (c.735A>C). In one patient , the variant was shown to have occured de novo (Koudova 2009). Moreover, this v ariant has not been identified in large and broad populations by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS). Computational analyses ( biochemical amino acid properties, conservation, AlignGVGD, PolyPhen2, and SIFT) do not provide strong support for or against an impact to the protein. In summa ry, this variant is likely pathogenic, though additional studies are required to fully establish its clinical significance. -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Mar 28, 2012

The L245F missense mutation in the BRAF gene has been published previously in association with Cardio-Facio-Cutaneous (CFC) Syndrome (Sarkozy et al., 2009). It has also been reported in an individual with LEOPARD syndrome and normal intelligence (Koudova et al., 2009). L245F results in a non-conservative amino acid substitution in that a small, compact Leucine residue is replaced with a large, bulky Phenylalanine at a position that is highly conserved. The variant is found in NOONAN panel(s). -

Noonan syndrome and Noonan-related syndrome Pathogenic:1

Pathogenic, reviewed by expert panel

curation

ClinGen RASopathy Variant Curation Expert Panel

May 10, 2019

The c.735A>T p.Leu245Phe variant in BRAF has been identified in at least 2 independent occurrences, one of which was de novo, in patients with clinical features of a RASopathy (PM6, PS4_Supporting; Partners LMM, University Magdeburg internal data; GTR Lab IDs: 21766, 506381 PMID: 19206169, 22190897). This variant was absent from large population studies (PM2; gnomAD, http://gnomad.broadinstitute.org). Computational prediction tools and conservation analysis suggest that the p.Leu245Phe variant may impact the protein (PP3). The variant is located in the BRAF 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). Of note, the p.Leu245Phe change has also been reported as a consequence of the c.735A>C variant in BRAF, which has been classified as pathogenic and therefore supports that this residue may be critical to protein function (PS1; ClinVar ID: 40347). 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 BRAF (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): PS4_Supporting, PM6, PM1, PM2, PS1, PP2, PP3. -

RASopathy Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jul 27, 2018

A different variant (c.735A>C) giving rise to the same protein effect observed here (p.Leu245Phe) has been reported in an individual affected with cardio-facio-cutaneous syndrome (PMID: 19416762), indicating that this residue may be critical for protein function. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has been observed in individuals affected with cardio-facio-cutaneous syndrome (PMID: 19206169, 22190897). ClinVar contains an entry for this variant (Variation ID: 40348). This variant is not present in population databases (ExAC no frequency). This sequence change replaces leucine with phenylalanine at codon 245 of the BRAF protein (p.Leu245Phe). The leucine residue is highly conserved and there is a small physicochemical difference between leucine and phenylalanine. -

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	0.99
BayesDel_addAF	Pathogenic	0.43	D
BayesDel_noAF	Pathogenic	0.38
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.90	.;.;D;.
Eigen	Uncertain	0.33
Eigen_PC	Uncertain	0.34
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Pathogenic	0.98	D;D;D;D
M_CAP	Pathogenic	0.41	D
MetaRNN	Pathogenic	0.92	D;D;D;D
MetaSVM	Uncertain	0.53	D
MutationAssessor	Benign	1.9	.;.;L;.
MutationTaster	Benign	1.0	D
PrimateAI	Pathogenic	0.92	D
PROVEAN	Uncertain	-2.8	.;.;.;D
REVEL	Pathogenic	0.83
Sift	Uncertain	0.0020	.;.;.;D
Sift4G	Uncertain	0.0040	.;.;.;D
Polyphen		0.82	.;.;P;.
Vest4		0.90
MutPred		0.83		Loss of ubiquitination at K240 (P = 0.1231);Loss of ubiquitination at K240 (P = 0.1231);Loss of ubiquitination at K240 (P = 0.1231);Loss of ubiquitination at K240 (P = 0.1231);
MVP		0.99
MPC		2.2
ClinPred		0.97	D
GERP RS		4.3
Varity_R		0.85
gMVP		0.88

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: rs397507466; hg19: chr7-140501337;