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_004333.4(BRAF):c.741T>G (p.Phe247Leu)

CA284654

55793 (ClinVar)

Gene: BRAF
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: 66924744-6ed6-4985-8479-1c8bab448ed0
Approved on: 2019-05-10
Published on: 2019-06-28

HGVS expressions

NM_004333.4:c.741T>G
NM_004333.4(BRAF):c.741T>G (p.Phe247Leu)
NC_000007.14:g.140801531A>C
CM000669.2:g.140801531A>C
NC_000007.13:g.140501331A>C
CM000669.1:g.140501331A>C
NC_000007.12:g.140147800A>C
NG_007873.3:g.128234T>G
NM_001354609.1:c.741T>G
NM_004333.5:c.741T>G
NR_148928.1:n.1046T>G
ENST00000288602.10:c.741T>G
ENST00000497784.1:n.776T>G
More

Pathogenic

Met criteria codes 8
PS2 PS3 PP2 PP3 PM1 PM6 PM2 PS4_Supporting
Not Met criteria codes 15
BA1 BS2 BS3 BS1 BS4 BP1 BP4 BP2 BP3 BP5 BP7 PS1 PP1 PM4 PM5

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.741T>G (p.Phe247Leu) variant in BRAF has been reported in the literature as a confirmed and unconfirmed de novo occurrence in 2 patients with clinical features of a RASopathy (PM6, PS2, PS4_Supporting; GeneDx internal data; GTR Lab ID 26957; SCV000077236.10). In vitro functional studies provide some evidence that the p.Phe247Leu variant may impact protein function (PS3; PMID: 28512244). 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). This variant was absent from large population studies (PM2; gnomAD, http://gnomad.broadinstitute.org). 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). Computational prediction tools and conservation analysis suggest that the p.Phe247Leu variant may impact 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): PM6, PS2, PS3, PM1, PM2, PP2, PP3, PS4_Supporting.
Met criteria codes
PS2
GeneDx: patient with clincial features of RASopathy in confirmed de novo occurrence.
PS3
Variant alters the RAS MAPK pathway (ERK phosphorylation) PMID: 28512244

PP2
Variant in BRAF
PP3
Variant REVEL score 0.816
PM1
Variant is located in exon 6
PM6
GeneDx: 1 patient diagnosed with CFC
PM2
Variant is absent from gnomAD
PS4_Supporting
GeneDx: 2 patients with RASopathies
Not Met criteria codes
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
NM_004333.4(BRAF):c.739T>C (p.Phe247Leu) met pathogenic, can't apply to this variant per circular argument issue
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.