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

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Variant: NM_004333.6(BRAF):c.1799T>G (p.Val600Gly)

CA281998

40389 (ClinVar)

Gene: BRAF
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: 33e1b46e-d087-4f11-a5d3-ab591b3261a1

HGVS expressions

NM_004333.6:c.1799T>G
NM_004333.6(BRAF):c.1799T>G (p.Val600Gly)
NM_004333.4:c.1799T>G
NM_001354609.1:c.1799T>G
NM_004333.5:c.1799T>G
NR_148928.1:n.2897T>G
NM_001354609.2:c.1799T>G
NM_001374244.1:c.1919T>G
NM_001374258.1:c.1919T>G
ENST00000288602.10:c.1799T>G
ENST00000479537.5:n.83T>G
ENST00000496384.6:n.622T>G
ENST00000497784.1:n.1834T>G
NC_000007.14:g.140753336A>C
CM000669.2:g.140753336A>C
NC_000007.13:g.140453136A>C
CM000669.1:g.140453136A>C
NC_000007.12:g.140099605A>C
NG_007873.3:g.176429T>G

Pathogenic

Met criteria codes 7
PM2 PM6 PM1 PS4_Supporting PS3 PP2 PP3

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The 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.
Met criteria codes
PM2
Absent from gnomAD v2.1.1 and v3
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
CR3 activation segment mutational hotspot
PS4_Supporting
PS3
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
REVEL: 0.925
Approved on: 2020-06-25
Published on: 2020-06-25
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