7-140778053-C-G

Variant summary

Our verdict is Pathogenic. Variant got 27 ACMG points: 27P and 0B. PS1_Very_Strong PM1 PM2 PM5 PP2 PP3_Strong PP5_Very_Strong

The NM_001374258.1(BRAF):c.1575G>C(p.Leu525Phe) variant causes a missense change. 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 nucleotide change resulting in same amino acid change has been previously reported as Pathogenicin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L525S) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: 𝑓 0.0 (0 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: BRAF NM_001374258.1 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:12 O:1
• Conservation: PhyloP100: 5.00

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]

(HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 27 ACMG points.

• PS1: Transcript NM_001374258.1 (BRAF) is affected with MISSENSE_VARIANT having same AA change as one Pathogenic present in ClinVar as 177844
• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 5 uncertain in NM_001374258.1
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr7-140778054-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 40370.Status of the report is reviewed_by_expert_panel, 3 stars.
• PP2: Missense variant where missense usually causes diseases, BRAF
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.943
• PP5: Variant 7-140778053-C-G is Pathogenic according to our data. Variant chr7-140778053-C-G is described in ClinVar as [Pathogenic]. Clinvar id is 13975.Status of the report is reviewed_by_expert_panel, 3 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BRAF	NM_001374258.1	c.1575G>C	p.Leu525Phe	missense_variant	13/20	ENST00000644969.2
BRAF	NM_004333.6	c.1455G>C	p.Leu485Phe	missense_variant	12/18	ENST00000646891.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BRAF	ENST00000644969.2	c.1575G>C	p.Leu525Phe	missense_variant	13/20		NM_001374258.1
BRAF	ENST00000646891.2	c.1455G>C	p.Leu485Phe	missense_variant	12/18		NM_004333.6	P4
	ENST00000700122.1	n.502+3185C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 152176 Hom.: 0 Cov.: 32 FAILED QC

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 31

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 152176 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 74346

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:12 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Aug 15, 2022	Published functional studies demonstrate a damaging effect with the variant causing a gain-of-function to the MAPK pathway (Niihori et al., 2006; Hu et al., 2015); 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 often considered pathogenic (HGMD); This variant is associated with the following publications: (PMID: 16439621, 18039235, 28972961, 24803665, 18413255, 23093928, 24458522, 25348715, 26150740, 26744778, 20301365, 28468735, 28524057, 22369373, 33753861, 32005694, 29493581, 19206169, 25194980, 16474404) -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Jul 13, 2023	The BRAF c.1455G>C; p.Leu485Phe variant (rs180177036) is reported in individuals with cardio-facio-cutaneous syndrome (Niihori 2006, Rodriguez-Viciana 2008, Sarkozy 2009). This variant is classified as pathogenic by an expert panel in the ClinVar database (Variation ID: 13975). It is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. Computational analyses predict that this variant is deleterious (REVEL: 0.757). In support of these predictions, functional analyses have demonstrated this variant has an impact on BRAF function (Niihori 2006, Rodriguez-Viciana 2008). Based on available information, the p.Leu485Phe variant is considered to be pathogenic. References: Niihori T et al. Germline KRAS and BRAF mutations in cardio-facio-cutaneous syndrome. Nat Genet. 2006 Mar;38(3):294-6. PMID: 16474404. Rodriguez-Viciana P, Rauen KA. Biochemical characterization of novel germline BRAF and MEK mutations in cardio-facio-cutaneous syndrome. Methods Enzymol. 2008;438:277-89. doi: 10.1016/S0076-6879(07)38019-1. PMID: 18413255. Sarkozy A et al. Germline BRAF mutations in Noonan, LEOPARD, and cardiofaciocutaneous syndromes: molecular diversity and associated phenotypic spectrum. Hum Mutat. 2009 Apr;30(4):695-702. PMID: 19206169. -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Aug 01, 2021	- -

RASopathy Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 19, 2024	This sequence change replaces leucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 485 of the BRAF protein (p.Leu485Phe). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with cardio-facio-cutaneous syndrome (PMID: 16474404, 19206169, 28524057). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 13975). 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 BRAF protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects BRAF function (PMID: 18413255). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, reviewed by expert panel	curation	ClinGen RASopathy Variant Curation Expert Panel	Feb 28, 2020	The c.1455G>C (p.Leu485Phe) variant in BRAF is absent from gnomAD (PM2). It has been detected in at least 4 patients with clinical features of a RASopathy, 1 of which was reported as a de novo case with parentage confirmation (PS4_Moderate; PS2; 19206169, 16474404, SCV000197149.4). In vitro functional studies provide some evidence that the p.L485F variant may impact protein function (PS3; PMID: 18413255). 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). Additionally, computational prediction tools and conservation analysis suggest that this variant may affect the protein (PP3). 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_Moderate, PS2, PS3, PM2, PP2, PP3. -
Pathogenic, criteria provided, single submitter	research	Division of Human Genetics, National Health Laboratory Service/University of the Witwatersrand	Jul 01, 2023	- -

Cardio-facio-cutaneous syndrome Pathogenic:1 Other:1

not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Sep 26, 2021	Variant summary: BRAF c.1455G>C (p.Leu485Phe) results in a non-conservative amino acid change located in the Protein kinase domain (IPR000719) of 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 251326 control chromosomes. c.1455G>C has been widely reported in the literature in individuals affected with Cardiofaciocutaneous Syndrome (example, Niihori_2006, Sarkozy_2009, Rodiguez-Viciana_2008). These data indicate that the variant is likely to be associated with disease. At least two publications report experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in an activated ERK pathway (Niihori_2006) and an increased kinase activity compared to wild-type in a MEK-ERK MBP phosphorylation assay (Rodriguez-Viciana_2008), both findings consistent with the established gain of function mechanism of disease. Multiple clinical diagnostic laboratories and an expert panel (ClinGen RASopathy Variant Curation Expert Panel) have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All submitters classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

Noonan syndrome;C1275081:Cardio-facio-cutaneous syndrome Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Oct 21, 2014

The c.1455G>C (p.Leu485Phe) variant in BRAF has been previously identified in fo ur individuals with clinical features of a RASopathy (Niihori 2006, Rodriguez-Vi ciana 2006, LMM unpublished data). It was absent from large population studies ( http://evs.gs.washington.edu/EVS/; dbSNP rs180177036). In addition, a different variant with the same amino acid change (c.1455G>T) was identified by our labora tory in one individual with Cardio-facio-cutaneous syndrome (CFC). In vitro func tional studies provide some evidence that the p.Leu485Phe variant may impact pro tein function by increasing its kinase activity (Rodriguez-Viciana 2008). Howeve r, these types of assays may not accurately represent biological function. In s ummary, this variant meets our criteria to be classified as pathogenic (http://p cpgmwww.partners.org/personalizedmedicince/LMM). -

Ataxia-telangiectasia syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

DASA

Mar 05, 2022

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change (ClinVar ID: 177844 - c.1575G>T;p.(Leu525Phe)) PS1.Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product (PMID: 18413255; 18953432) - PS3_moderate.The c.1455G>C;p.(Leu485Phe) missense variant has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 13975; PMID: 19206169; PMID: 18953432; PMID: 18039235; PMID: 16474404) - PS4. The variant is located in a mutational hot spot and/or critical and well-established functional domain (Pkinase_Tyr) - PM1. This variant is not present in population databases (rs180177036- gnomAD; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2. Pathogenic missense variant in this residue have been reported (ClinVar ID: 40370) - PM5. The variant was assumed de novo, but without confirmation of paternity and maternity (PMID: 19206169) - PM6. Missense variant in BRAF that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease - PP2. Multiple lines of computational evidence support a deleterious effect on the gene or gene product - PP3. In summary, the currently available evidence indicates that the variant is pathogenic. -

Cardiofaciocutaneous syndrome 1 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Mar 01, 2006

- -

BRAF-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 27, 2023

The BRAF c.1455G>C variant is predicted to result in the amino acid substitution p.Leu485Phe. This variant has been reported in individuals with cardio-facio-cutaneous syndrome (CFCS) (see for example Niihori et al. 2006. PubMed ID: 16474404). Additionally, a different nucleotide substitution (c.1455G>T) resulting in the same missense variant (Leu485Phe) has been reported in individuals with CFCS (Table S1 - Mohan et al. 2022. PubMed ID: 34358384). Functional studies demonstrate this variant results in increased p-MEK/ERK levels, consistent with a gain-of-function mechanism, resulting in hyperactivation of the RAS pathway (Rodriguez-Viciana et al. 2008. PubMed ID: 18413255). Additionally, a different missense substitution (p.Leu485Ser) affecting this residue has been reported as pathogenic (Aizaki et al. 2011. PubMed ID: 20395089). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as pathogenic. -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 09, 2021

The c.1455G>C (p.L485F) alteration is located in coding exon 12 of the BRAF gene. This alteration results from a G to C substitution at nucleotide position 1455, causing the leucine (L) at amino acid position 485 to be replaced by a phenylalanine (F). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This alteration was previously reported in multiple unrelated patients with cardio-facio-cutaneous (CFC) syndrome (Niihori, 2006; Rodriguez-Viciana, 2006; Yoon, 2007; Sarkozy, 2009). Parent-child trio confirmed the de novo occurrence of the c.1455G>C alteration in the patient reported by Sarkozy, et al. (2009). The patient reported by Rodriguez-Viciana et al. (2006) had the characteristic facies of CFC, developmental delay, hypotonia, hypertrophic cardiomyopathy, hair and skin anomalies, and other musculoskeletal, GI and ocular abnormalities. He was not reported to have short stature, seizures, or lymphadema. Another 7 year old boy with the p.L485F alteration had severe academic difficulty and multiple types of seizures, with onset at 2 weeks (Yoon, 2007). This amino acid position is highly conserved in available vertebrate species. Niihori et al. (2006) used luciferase assays to show that BRAF with the p.L485F mutation, when introduced into NIH3T3 cells, caused about a 2.5 fold increase in ELK1 transcription, indicating that it over-stimulated the ERK pathway compared to wild-type leading to increased kinase activity. Rodriguez-Viciana and Rauen (2008) introduced Flag-tagged BRAF p.L485F mutant into 293T cells and found about 1.8 fold increase in its kinase activity by two different methods namely a coupled MEK-ERK-MBP phosphorylation assay and western blotting by probing with antibodies that specifically detect phosphorylated ERK and MEK. This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.40	D
BayesDel_noAF	Pathogenic	0.34
Cadd	Uncertain	24
Dann	Uncertain	1.0
Eigen	Uncertain	0.20
Eigen_PC	Uncertain	0.26
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Pathogenic	0.99	D;D;D;D
M_CAP	Uncertain	0.087	D
MetaRNN	Pathogenic	0.94	D;D;D;D
MetaSVM	Benign	-0.70	T
MutationTaster	Benign	1.0	A
PrimateAI	Pathogenic	0.90	D
Polyphen		0.26	.;.;B;.
MutPred		0.86		Gain of catalytic residue at L485 (P = 0.046);.;Gain of catalytic residue at L485 (P = 0.046);.;
MVP		0.99
MPC		2.1
ClinPred		0.99	D
GERP RS		4.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.95
gMVP		0.81

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: rs180177036; hg19: chr7-140477853;