The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_004333.6(BRAF):c.1406G>A (p.Gly469Glu)

CA279970

13974 (ClinVar)

Gene: BRAF
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: f75f3f8b-6c9c-41a1-9cee-4716d67229dd
Approved on: 2024-09-17
Published on: 2024-10-01

HGVS expressions

NM_004333.6:c.1406G>A
NM_004333.6(BRAF):c.1406G>A (p.Gly469Glu)
NC_000007.14:g.140781602C>T
CM000669.2:g.140781602C>T
NC_000007.13:g.140481402C>T
CM000669.1:g.140481402C>T
NC_000007.12:g.140127871C>T
NG_007873.3:g.148163G>A
ENST00000646891.2:c.1406G>A
ENST00000288602.11:c.1526G>A
ENST00000479537.6:c.76G>A
ENST00000496384.7:c.1406G>A
ENST00000497784.2:c.*856G>A
ENST00000642228.1:c.*484G>A
ENST00000642875.1:n.848G>A
ENST00000644120.1:n.1796G>A
ENST00000644650.1:c.502G>A
ENST00000644905.1:n.1495G>A
ENST00000644969.2:c.1526G>A
ENST00000646334.1:n.536G>A
ENST00000646730.1:c.1406G>A
ENST00000646891.1:c.1406G>A
ENST00000647434.1:c.449G>A
ENST00000288602.10:c.1406G>A
ENST00000496384.6:c.229G>A
ENST00000497784.1:c.1441G>A
NM_004333.4:c.1406G>A
NM_001354609.1:c.1406G>A
NM_004333.5:c.1406G>A
NR_148928.1:n.1711G>A
NM_001354609.2:c.1406G>A
NM_001374244.1:c.1526G>A
NM_001374258.1:c.1526G>A
NM_001378467.1:c.1415G>A
NM_001378468.1:c.1406G>A
NM_001378469.1:c.1340G>A
NM_001378470.1:c.1304G>A
NM_001378471.1:c.1295G>A
NM_001378472.1:c.1250G>A
NM_001378473.1:c.1250G>A
NM_001378474.1:c.1406G>A
NM_001378475.1:c.1142G>A
More

Pathogenic

Met criteria codes 7
PM2_Supporting PS3_Supporting PS4 PP2 PP3 PM1 PS2_Very Strong

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for BRAF Version 2.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.1406G>A variant in BRAF is a missense variant predicted to cause substitution of glycine by glutamic acid at amino acid 469 (p.Gly469Glu). This variant is absent from gnomAD v4 (PM2_Supporting). 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). The REVEL computational prediction analysis tool produced a score of 0.921, which is above the threshold necessary to apply PP3 (PP3). Furthermore, this variant is in a location which has been defined by the ClinGen RASopathy Expert Panel functional domain of BRAF (PM1). This variant has been reported in the literature in at least 12 patients with clinical features of RASopathy (PS4, PMIDs: 18042262, 16474404, 30141192, 29907801, 35418823), out of which 3 patients were reported as a confirmed de novo occurrence (PS2_VeryStrong; PMIDs: 18042262, 16474404). Luciferase assays showed that p.Gly469Glu did not enhance ELK-dependent transcription indicating that this variant impacts protein function (PS3_Supporting; 16474404). In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant RASopathies based on the ACMG/AMP criteria applied, as specified by the ClinGen RASopathy Variant Curation Expert Panel: PS2_VeryStrong, PS4, PM1, PS3_Supporting, PM2_Supporting, PP2, PP3 (Specification Version 2.1, 9/17/2024)
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v4
PS3_Supporting
Luciferase assays showed that p.Gly469Glu did not enhance ELK-dependent transcription indicating that this variant impacts protein function (PMID:16474404)
PS4
This variant has been reported in the literature in at least 7 patients with clinical features of RASopathy (PMIDs: 18042262, 16474404, 30141192, 29907801, 35418823)
PP2
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
PP3
The REVEL computational prediction analysis tool produced a score of 0.921, which is above the threshold necessary to apply PP3
PM1
This variant is in a location which has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of BRAF (PMID 29493581).
PS2_Very Strong
The p.G469E variant in BRAF has been reported in the literature as a confirmed de novo occurrence in 3 patients with clinical features of a RASopathy (PMIDs: 18042262, 16474404).
Curation History
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