NM_001374258.1:c.1575G>T
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PS4PS3PM2PP3PP2PM6_Strong
This summary comes from the ClinGen Evidence Repository: The c.1455G>T (p.Leu485Phe) variant in BRAF is absent from gnomAD (PM2). It has been detected in at least 5 patients with clinical features of a RASopathy, 2 of which were reported as unconfirmed de novo cases (PS4; PM6_Strong; PMIDs: 18039235, 28524057, SCV000832735.1, SCV000204150.4, SCV000965953.1, Otto-von-Guericke-Universität Magdeburg internal communication). In vitro functional studies provide some evidence that the p.L485F variant may impact protein function (PS3; PMID:18413255). 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). Additionally, computational prediction tools and conservation analysis suggest that this variant may affect 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): PS4, PM6_Strong, PS3, PM2, PP2, PP3. LINK:https://erepo.genome.network/evrepo/ui/classification/CA280060/MONDO:0021060/004
Frequency
Consequence
NM_001374258.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BRAF | ENST00000644969.2 | c.1575G>T | p.Leu525Phe | missense_variant | Exon 13 of 20 | NM_001374258.1 | ENSP00000496776.1 | |||
BRAF | ENST00000646891.2 | c.1455G>T | p.Leu485Phe | missense_variant | Exon 12 of 18 | NM_004333.6 | ENSP00000493543.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
RASopathy Pathogenic:2
This variant is not present in population databases (ExAC no frequency). This sequence change replaces leucine with phenylalanine at codon 485 of the BRAF protein (p.Leu485Phe). The leucine residue is highly conserved and there is a small physicochemical difference between leucine and phenylalanine. This missense change has been observed in individuals with cardio-facio-cutaneous syndrome (PMID: 16439621, 16474404, 18039235, 19206169, 28524057). ClinVar contains an entry for this variant (Variation ID: 177844). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). Experimental studies have shown that this missense change affects BRAF function (PMID: 16439621, 16474404, 18413255, 25348715). For these reasons, this variant has been classified as Pathogenic. -
The c.1455G>T (p.Leu485Phe) variant in BRAF is absent from gnomAD (PM2). It has been detected in at least 5 patients with clinical features of a RASopathy, 2 of which were reported as unconfirmed de novo cases (PS4; PM6_Strong; PMIDs: 18039235, 28524057, SCV000832735.1, SCV000204150.4, SCV000965953.1, Otto-von-Guericke-Universität Magdeburg internal communication). In vitro functional studies provide some evidence that the p.L485F variant may impact protein function (PS3; PMID: 18413255). 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). Additionally, computational prediction tools and conservation analysis suggest that this variant may affect 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): PS4, PM6_Strong, PS3, PM2, PP2, PP3. -
Noonan syndrome;C1275081:Cardio-facio-cutaneous syndrome Pathogenic:1
The c.1455G>T (Leu485Phe) variant in BRAF has been previously identified in one individual with clinical features of a Cardio-facio-cutaneous syndrome (LMM unpu blished data). It was absent from large population studies (http://evs.gs.washin gton.edu/EVS/). In addition, a different variant with the same amino acid change (c.1455G>C) was identified in four individuals with clinical features of a RASo pathy (Niihori 2006, Rodriguez-Viciana 2006, LMM unpublished data). In vitro fu nctional studies provide some evidence that the Leu485Phe variant may impact pro tein function by increasing its kinase activity (Rodriguez-Viciana 2008). Howeve r, these types of assays may not accurately represent biological function. In s ummary, this variant meets our criteria to be classified as pathogenic (http://p cpgmwww.partners.org/personalizedmedicince/LMM). -
Cardiofaciocutaneous syndrome 1 Pathogenic:1
PS1, PS4, PM1, PM2, PP3, PP5- The variant has been reported in ClinVar as Pathogenic by other laboratories (Variation ID: 177844). In silico prediction tools estimated that the variant could be damaging for the protein function/stracture. It is not present in population databases (gnomAD no frequency). -
Cardio-facio-cutaneous syndrome Pathogenic:1
Variant summary: BRAF c.1455G>T (p.Leu485Phe) results in a non-conservative amino acid change located in the Serine-threonine/tyrosine-protein kinase, catalytic domain (IPR001245) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251326 control chromosomes (gnomAD). The variant, c.1455G>T, has been reported in the literature in individuals affected with Cardiofaciocutaneous Syndrome (Rodriguez-Viciana_2006, Sato_2017). Another variant (c.1455G>C) leading to the same protein change (p.Leu485Phe) has also been observed in individuals affected with Cardiofaciocutaneous Syndrome including one de novo occurrence (Niihori_2006, Sarkozy_2009). These data indicate that the variant is likely to be associated with disease. At least two publications reported experimental evidence evaluating an impact on protein function and showed increased BRAF activity (Niihori_2006, Rodriguez-Viciana_2006). One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as likely pathogenic. Another variant affecting the same codon, p.L485S, has been reported to associate with Cardiofaciocutaneous Syndrome too. Based on the evidence outlined above, the variant was classified as pathogenic. -
not provided Pathogenic:1
Reported in probands with clinical features of cardio-facio-cutaneous (CFC) syndrome (Yoon et al., 2007; Sato et al., 2017; Mohan et al., 2022); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Missense variants in this gene are often considered pathogenic (HGMD); This variant is associated with the following publications: (PMID: 34358384, 30406758, 18039235, 28524057) -
Noonan syndrome Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at