The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

  • See Evidence submitted by expert panel for details.

Variant: NM_004333.6(BRAF):c.1455G>C (p.Leu485Phe)

CA273414

13975 (ClinVar)

Gene: BRAF
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: d7b34568-d590-44cf-a60c-e208532866d3
Approved on: 2020-02-27
Published on: 2020-04-09

HGVS expressions

NM_004333.6:c.1455G>C
NM_004333.6(BRAF):c.1455G>C (p.Leu485Phe)
NC_000007.14:g.140778053C>G
CM000669.2:g.140778053C>G
NC_000007.13:g.140477853C>G
CM000669.1:g.140477853C>G
NC_000007.12:g.140124322C>G
NG_007873.3:g.151712G>C
NM_004333.4:c.1455G>C
NM_001354609.1:c.1455G>C
NM_004333.5:c.1455G>C
NR_148928.1:n.1760G>C
NM_001354609.2:c.1455G>C
NM_001374244.1:c.1575G>C
NM_001374258.1:c.1575G>C
ENST00000288602.10:c.1455G>C
ENST00000496384.6:n.278G>C
ENST00000497784.1:n.1490G>C
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Pathogenic

Met criteria codes 6
PS4_Moderate PS2 PS3 PP2 PP3 PM2
Not Met criteria codes 1
PM5

Evidence Links 3

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
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.
Met criteria codes
PS4_Moderate
LMM unpublished (SCV000197149.4) + PMID: 16474404

PS3
PMID 18413255: Kinase activities of selected B-Raf missense CFC mutations are compared to known B-Raf mutations found in cancer. Empty vector, wildtype B-Raf (WTB-Raf) or the indicated B-Raf point mutants were transfected in 293Tcells, and B-Raf activity was measured on Flag-immunoprecipitates using a coupled MEK-ERK-MBP phosphorylation assay. L485F showed increased kinase activity compared to WT

PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
REVEL: .757, no predicted splicing impact, evolutionarily conserved
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Not Met criteria codes
PM5
ClinVar 40370 (Likely Path)
Curation History
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