Genetic Information
Gene & Transcript Details
| ID | Status | Details |
|---|---|---|
| NM_001354609.2 | Alternative | 9687 nt | 227–2530 |
| NM_001354609.1 | Alternative | 9702 nt | 226–2529 |
Variant Details
Clinical & Population Data
Population Frequency
gnomADClinVar
OpenThe c.1799T>G (p.Val600Gly) variant in BRAF is absent from gnomAD (PM2). It has been identified in one individual with Cardiofaciocutaneous syndrome (PS4_Supporting; PMID: 20735442). It has also been reported in the literature as an unconfirmed de novo occurrence (PM6; GeneDx internal communication). In vitro functional studies provide some evidence that the p.Val600Gly variant may impact protein function (PS3; PMID: 20735442). 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). Computational prediction tools and conservation analysis suggest that the p.Val600Gly variant may impact the protein (PP3). Finally, the variant is located in BRAF, 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). 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): PS3, PM1, PM2, PM6, PS4_Supporting, PP3, PP2.
This sequence change replaces valine, which is neutral and non-polar, with glycine, which is neutral and non-polar, at codon 600 of the BRAF protein (p.Val600Gly). 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: 20735442). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 40389). Invitae Evidence Modeling incorporating data from in vitro experimental studies (internal data) indicates that this missense variant is expected to disrupt BRAF function with a positive predictive value of 95%. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
"This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratories) and as Pathogenic (1 clinical laboratories) and as Pathogenic by ClinGen RASopathy Variant Curation Expert Panel expert panel."
COSMIC Somatic Evidence
Open
Functional Impact & Domains
Functional Domain
Error in OpenAI Consolidation. OncoKB: BRAFV600GBRAFV600GSomaticNCBI Gene:673|Show additional gene information Variant OverviewBRAF, an intracellular kinase, is frequently mutated in melanoma, thyroid and lung cancers among others.The BRAF V600G mutation is likely oncogenic.Hide mutation effect description The class I (PMID: 28783719) activating exon 15 BRAF V600G mutation is located in the kinase domain of the protein. This mutation has been found in cardio-facio-cutaneous syndrome (CFC), lung cancer and esophagogastric cancer (PMID: 26287849). Substitutions at position V600 of BRAF, including the common BRAF V600E mutation, are known to be activating and oncogenic (PMID: 12068308, 16273091, 15035987). Expression of this mutation in 293T cells demonstrated that this mutation is activating as measured by increased downstream ERK activation and increased transcription of downstream MAPK pathway transcriptional targets (e.g. ELK) compared to wildtype BRAF (PMID: 20735442). A patient with non-small cell lung cancer (NSCLC) harboring the BRAF V600G mutation had stable disease in response to treatment with vemutafenib, while a patient with sarcoma and a patient with esophagogastric cancer both harboring the BRAF V600G mutation had progressive disease in response to vemurafenib (PMID: 26287849). JAX-CKB: BRAF V600G (previously reported as V599G) lies within the activation segment of the kinase domain of the Braf protein (PMID: 15035987). V600G confers a gain of function to Braf as indicated by increased phosphorylation of BRAF and downstream MEK and ERK and activation of ELK in culture (PMID: 20735442, PMID: 26744778), and in one of two cell lines, increased cell proliferation and viability compared to wild-type Braf (PMID: 29533785).
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Computational Analysis
Pathogenicity Predictions
SpliceAISpliceAI Scores
Window: ±500bp| Effect Type | Score | Position |
|---|---|---|
| Acceptor Loss (AL) | 0.07 | 57 bp |
| Donor Loss (DL) | 0.11 | -61 bp |
| Acceptor Gain (AG) | 0.0 | 0 bp |
| Donor Gain (DG) | 0.0 | 22 bp |
VCEP Guidelines
Applied ACMG/AMP Criteria (VCEP Specific)
PS3 (Unknown (Pre-LLM))
From pre-LLM assessment (LLM Failed)
PM2 (Unknown (Pre-LLM))
From pre-LLM assessment (LLM Failed)
PP5 (Unknown (Pre-LLM))
From pre-LLM assessment (LLM Failed)
BP4 (Unknown (Pre-LLM))
From pre-LLM assessment (LLM Failed)