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.739T>G (p.Phe247Val)

CA135140

44830 (ClinVar)

Gene: BRAF
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: d691f327-120d-4c5c-b56e-fbfdc3f820f3
Approved on: 2019-05-10
Published on: 2019-06-28

HGVS expressions

NM_004333.4:c.739T>G
NM_004333.4(BRAF):c.739T>G (p.Phe247Val)
NC_000007.14:g.140801533A>C
CM000669.2:g.140801533A>C
NC_000007.13:g.140501333A>C
CM000669.1:g.140501333A>C
NC_000007.12:g.140147802A>C
NG_007873.3:g.128232T>G
NM_001354609.1:c.739T>G
NM_004333.5:c.739T>G
NR_148928.1:n.1044T>G
ENST00000288602.10:c.739T>G
ENST00000497784.1:n.774T>G

Likely Pathogenic

Met criteria codes 5
PS4_Supporting PP2 PP3 PM1 PM2
Not Met criteria codes 18
BS2 BS4 BS1 BS3 BP1 BP4 BP2 BP3 BP5 BP7 PS3 PS1 PS2 BA1 PP1 PM5 PM4 PM6

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.739T>G (p.Phe247Val) variant in BRAF has been identified in at least 2 independent occurrences in patients with clinical features of a RASopathy (PS4_Supporting; Partners LMM, GeneDx internal data; GTR Lab IDs 21766, 26957; ClinVar SCV000061624.5, SCV000330320.6). 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). 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). A different pathogenic missense variant (p.Phe247Leu) has been previously identified at this codon of BRAF which may indicate that this residue is critical to the function of the protein (PM5 not usable due to PM1 application; ClinVar 180784, 55793). Computational prediction tools and conservation analysis suggest that the p.Phe247Val variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Supporting, PM2, PM1, PP2, PP3.
Met criteria codes
PS4_Supporting
The p.Phe247Val variant (no c.DNA change specified) was identified in a patient with CFC in a thesis by Wright et al. 2013 and was reported as a Manchester Centre for Genomic Medicine (MCGM) unpublished case. LMM: Daughter affected with NS (postive for variant). Mother was negative for variant and unaffected. Father not available for testing. Patient's phenotype may be consistent with CFC phenotype though more information may be needed. GeneDx: no case evidence for pathogenicity
PP2
Variant is in BRAF
PP3
REVEL score of 0.921
PM1
ex6, ex11, P-loop (AA 459-474); CR3 activation segment (AA 594-627) Variant is located in exon 6 of the NM_004333.5 transcript which has been specified by the RAS VCEP as a hotspot
PM2
Variant absent in gnomAD
Not Met criteria codes
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
LMM: A mother unaffected with NS (negative for variant) had a daughter affected with NS (postive for variant).
BS1
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
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
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
p.Phe247Leu variant has been identified in patients in two different cDNA changes. c.739T>C is Pathogenic. However, PM1 has already been used so this code cannot be applied.
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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