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.1391G>A (p.Gly464Glu)

CA250636

13964 (ClinVar)

Gene: BRAF
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: 2731c1d0-461e-451c-b70b-9882166c553c

HGVS expressions

NM_004333.6:c.1391G>A
NM_004333.6(BRAF):c.1391G>A (p.Gly464Glu)
NM_004333.4:c.1391G>A
NM_001354609.1:c.1391G>A
NM_004333.5:c.1391G>A
NR_148928.1:n.1696G>A
NM_001354609.2:c.1391G>A
NM_001374244.1:c.1511G>A
NM_001374258.1:c.1511G>A
ENST00000288602.10:c.1391G>A
ENST00000496384.6:n.214G>A
ENST00000497784.1:n.1426G>A
NC_000007.14:g.140781617C>T
CM000669.2:g.140781617C>T
NC_000007.13:g.140481417C>T
CM000669.1:g.140481417C>T
NC_000007.12:g.140127886C>T
NG_007873.3:g.148148G>A

Pathogenic

Met criteria codes 8
PS2 PS3 PS4_Supporting PP2 PP3 PM1 PM2 PM6
Not Met criteria codes 1
PM5

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.1391G>A (p.Gly464Glu) variant in BRAF has been observed in 2 probands with phenotypes consistent with cardiofaciocutaneous syndrome (PS4_Supporting; LMM internal data, SCV000197160.4; GeneDx internal data, SCV000057209.13). One of these cases was de novo with maternity and paternity confirmed, while the other was de novo without confirmation of maternity or paternity (PS2, PM6). The p.Gly464Glu variant was absent from large population studies (PM2; gnomad.broadinstitute.org). In vitro functional assays indicate that this variant may impact protein function (PS3; PMID: 25155755). It occurs in the P-loop domain of the protein, which has been identified as an important region for protein function (PM1; 29493581). Computational prediction tools and conservation analyses also suggest that this variant may impact the protein (PP3). 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 variants are common (PP2; PMID: 29493581). Of note, this variant has also been observed in association with somatic malignancies; however, analysis and classification of somatic variation is currently not used to inform germline classifications for the RASopathies. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant RASopathy. RASopathy-specific ACMG/AMP criteria applied: PS2, PS3, PS4_Supporting, PM1, PM2, PM6, PP2, PP3.
Met criteria codes
PS2
Observed by GeneDx in 1 de novo case via whole exome trio. The expert panel believed that the patient's detailed phenotypic information was consistent with CFC syndrome (SCV000057209.13).
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4_Supporting
Observed in 2 probands with phenotypes consistent with cardiofaciocutaneous syndrome (LMM internal data, SCV000197160.4; GeneDx internal data, SCV000057209.13).
PP2
BRAF is a missense-constrained gene.
PP3
REVEL score 0.949. Highly conserved (no animals in UCSC database have an alternative amino acid at this site). Splicing is not predicted to be impacted by Alamut.
PM1
Occurs in the P-loop domain (AA 459-474).
PM2
Absent from gnomAD v2 and v3.
PM6
Observed in 1 individual heterozygous for this variant diagnosed with CFC. Mother and father were negative for the variant and unaffected (LMM internal data; SCV000197160.4).
Not Met criteria codes
PM5
Not applied since PM1 is already met. ClinVar contains 4 other variants in this codon (1 LP, 3 P), but none have been assessed by the VCEP at this point.
Approved on: 2020-03-09
Published on: 2020-03-09
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