The BRAF NM_004333.6:c.1801A>G (NP_004324.2:p.(Lys601Glu)) missense variant has previously been reported in somatic cancers (COSMIC; COSV56058494, n = 208 times), and lies in a statistically significant hotspot (cancerhotspots.org). Based on available guidelines, this variant is considered to be a Variant of Uncertain Significance (VUS).
Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.
Uncertain.The recorded classification is uncertain significance.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.BRAF encodes a protein kinase that helps control the MAPK/ERK signaling pathway, which regulates cell growth, division, and specialization. Changes in BRAF are associated with cardiofaciocutaneous, Noonan, and Costello syndromes. BRAF is an oncogene, and abnormal activation of its signaling can drive cancers including melanoma, thyroid cancer, colorectal cancer, lung cancer, lymphoma, and hairy cell leukemia.
The recorded framework is ClinGen BRAF VCEP v2.3. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
The applied criteria and their strengths are shown as assessed under the stated framework.
Met, Moderate: residue 601 falls within the VCEP-approved CR3 activation segment spanning residues 594-627.
Met: VCEP REVEL score 0.916 is above the PP3 missense threshold of ≥0.7.
No benign criterion marked as applied in the recorded assessment.
VUS: PM1 (moderate) and PP3 (supporting) are met, but no BRAF VCEP v2.3 pathogenic or benign combination rule is satisfied.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 1 / 1,612,884 alleles. Recorded AF 6.20007e-07. Recorded homozygote count 0.
This variant is present in gnomAD v2.1 (AF= 3.98004e-06; MAF= 0.00040%, 1/251254 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.80049e-06; MAF= 0.00088%, 1/113630 alleles, homozygotes = 0).
Not available in gnomAD-Canada v1.0.
Recorded REVEL score: 0.916. Refer to the recorded PP3/BP4 rationale for interpretation.
1 Likely pathogenic · 1 Pathogenic. ClinVar API review status: criteria provided, single submitter.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Oncogenic.
This variant has previously been reported in somatic cancers (COSMIC; COSV56058494, n = 208 times).
This variant lies in a statistically significant hotspot.
ACMG/AMP criteria under ClinGen BRAF VCEP v2.3, with the data and sources behind each one.
28 criteria with recorded statuses: 2 met · 4 not met · 12 not assessed · 10 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
PVS1, PM4, and BP3 are not applicable under the governing BRAF VCEP specification for this missense variant.
PM1 is met at Moderate strength because Lys601 lies in the VCEP-approved CR3 activation segment (AA 594-627).
PS1, PM5, and PP2 are not assessed because their required pathogenic comparator, same-codon comparator, and missense z-score evidence respectively are unavailable under the VCEP rules.
BP1 is not applicable because the variant is missense and the VCEP limits BP1 to specified truncating variants.
Within the requested phenotype/prevalence group, PS4 and BP5 are not assessed because the available evidence does not provide the germline RASopathy phenotype-specific counts or VCEP point assignments required by their rules.
PP4, PP5, and BP6 are not applicable because the BRAF VCEP explicitly excludes them or directs their evidence to PS4.
No criteria match.
Residue 601 lies within the VCEP-defined CR3 activation segment, residues 594-627. The VCEP limits PM1 to critical, well-established functional domains in the supplementary table, and this missense variant is within that approved domain; the rule also excludes specific-residue use under PM1, which is not needed here. The searched RAF-Alignment.xlsx text contains no entry for c.1801A>G, p.Lys601Glu, or p.K601E, but the domain rule independently establishes applicability.
Applicable only to critical and well-established functional domains available in the supplementary table (exon 6, exon 11, P-loop [AA 459-474], CR3 activation segment [AA 594-627]). Not applicable to specific amino acid residues (see PM5).
This is a missense variant, NP_004324.2:p.(Lys601Glu). The governing BRAF VCEP rule specifies the missense PP3 path as REVEL ≥0.7; the REVEL lookup reports 0.916, so PP3 is met at Supporting strength. The available SpliceAI result is not used for this missense PP3 path because the governing rule names REVEL for missense variants, and the same prediction is not counted again under BP4 or BP7.
For missense variants: REVEL ≥ 0.7. For splicing impact, predicted outcome must match disease mechanism.
The governing BRAF VCEP applies PM2 at supporting strength when the variant is absent from controls in gnomAD. The variant is present in the default all-comers gnomAD datasets: gnomAD v2.1 reports 1/251254 alleles (AF 3.98003613872814e-06; homozygotes 0), and gnomAD v4.1 reports 1/1612884 alleles (AF 6.200073904880946e-07; homozygotes 0). Because the VCEP rule says gnomAD without specifying a non-cancer or exome-only subset, these all-comers observations prevent PM2; the criterion is not met.
The variant must be absent from controls (gnomAD).
The governing BRAF VCEP sets BA1 at a gnomAD filtering allele frequency of at least 0.05%. The highest observed all-comers population frequency is 0.00398% in gnomAD v2.1 European (non-Finnish) exomes (1/251254 alleles; overall AF 0.000398%), and gnomAD v4.1 has a highest observed population frequency of 0.00338% in Ashkenazi Jewish individuals (1/29,572 alleles; overall AF 0.000062%). Both are below 0.05%, so BA1 is not met.
GnomAD filtering allele frequency ≥0.05%.
The governing BRAF VCEP sets BS1 at a gnomAD filtering allele frequency of at least 0.025%. The highest observed all-comers population frequency is 0.00398% in gnomAD v2.1 European (non-Finnish) exomes, and the highest observed gnomAD v4.1 population frequency is 0.00338% in Ashkenazi Jewish individuals. Both are below 0.025%, so BS1 is not met.
GnomAD filtering allele frequency ≥0.025%.
This is a missense variant, so the governing BRAF VCEP missense BP4 path applies and names REVEL with a cutoff of ≤0.3. The REVEL lookup reports 0.916, which exceeds that cutoff; therefore BP4 is not met. SpliceAI is not substituted for the VCEP's named missense predictor and is not double-counted with PP3.
For missense variants: REVEL ≤0.3.
The VCEP rule requires the same amino acid change as a previously established pathogenic variant. PMID:22608338 directly reports BRAF K601E, but the available source establishes clinical observation and treatment outcome rather than independently establishing pathogenicity under this VCEP; no qualifying pathogenic comparator with a documented criterion-level basis was identified.
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. Applicable for observed analogous residue positions in _BRAF_ and _RAF1_.
The VCEP permits PS2 based on de novo point scoring, but the available evidence does not document a germline de novo observation for NM_004333.6:c.1801A>G, confirmation of both maternity and paternity, the proband's RASopathy phenotype, or absence of family history; the fetched reports concern somatic tumors and cannot establish this criterion.
The BRAF VCEP requires well-established functional studies and calibrates PS3 as Supporting for one approved assay or Moderate for two or more different approved assays. The governing approved-functional-studies file contains no entry for this variant under c.1801A>G, p.Lys601Glu, or p.K601E. The reviewed literature reports K601E clinical treatment outcomes but does not provide a qualifying approved BRAF functional assay result for this variant. Therefore PS3 cannot be assigned from the available evidence.
ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for BRAF Version 2.3: PS3 functional assay strength calibration.
The BRAF VCEP makes PS4 applicable to autosomal-dominant cases with RASopathy phenotypic specifications and assigns strength from points. The available literature concerns somatic cancer cohorts, not germline RASopathy patients: PMID:12198537 reports one BRAF K600E/K601E-equivalent tumor among 330 colorectal tumors, and PMID:22608338 reports two K601E melanoma patients in a treatment study. Neither provides a germline RASopathy case-control comparison, unaffected-control count, or VCEP PS4 point assignment. The available gnomAD observation is one allele among 1,612,884 alleles in v4.1, but no comparable affected RASopathy case frequency is available; therefore an OR and confidence interval cannot be validly calculated for this criterion.
Strength adjustment using point-based scoring for autosomal dominant cases with phenotypic specifications: full points awarded with RASopathy phenotypes, reduced points applicable to cases with minimal phenotypic information (i.e. prenatal cases, cases with a clinical order of a RASopathy panel without clinical information, and cases with limited clinical information in other global tests (such as WES)). ... The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... ≥5 points. ... ≥3 points. ... ≥1 points.
The VCEP permits moderate PM5 for one likely pathogenic residue change at the same codon and strong PM5 for at least two different likely pathogenic residue changes at the same codon observed in at least five probands. The available PM5 candidate search returned zero same-residue candidates, so the required comparator evidence is unavailable rather than disproven.
1 [likely] pathogenic residue change at the same codon.
The VCEP permits PM6 based on assumed de novo point scoring without confirmed maternity and paternity, with phenotype-dependent adjustment, but the available evidence contains no germline de novo observation, parental testing result, or documented RASopathy phenotype for this variant; somatic tumor reports are insufficient.
The VCEP requires informative meioses for PP1 and recommends segregation in more than one family, but the available evidence documents no affected relatives, parental segregation, or informative meioses for NM_004333.6:c.1801A>G.
The VCEP requires a missense z score greater than 3.09 in gnomAD. The case evidence contains no BRAF missense z score, so this threshold cannot be evaluated without substituting an unapproved population metric.
Missense z score is >3.09 in gnomAD.
The governing BRAF VCEP defines BS2 only through its point-based rules of -4 points or -1 point. The available population data show zero homozygotes in gnomAD v2.1 and v4.1, but the VCEP text supplied here does not define a conversion from gnomAD homozygote counts to BS2 points, and no qualifying healthy-adult observation with a VCEP point value is available. BS2 therefore cannot be evaluated without importing a non-VCEP rule.
-4 Points. ... -1 Point.
The VCEP requires one informative meiosis for BS4, but the available evidence contains no affected-family-member non-segregation observation, no informative meiosis, and no information addressing phenocopies or multiple pathogenic variants in the family.
The BRAF VCEP Version 2.3 CSPEC provides BP2 strength thresholds of at least (-1), (-2), or (-4) point(s), but the available case evidence contains no qualifying observation of this variant with another pathogenic variant in cis or trans, no affected-proband allelic observation, and no phase or inheritance data from which the required point value can be established. BP2 therefore cannot be evaluated without substituting a non-VCEP rule.
≥ (-4) Points. ... ≥ (-2) Points. ... ≥ (-1) Point.
The BRAF VCEP requires BP5 points for an alternative molecular cause of a RASopathy in a different gene, or for a phenotype inconsistent with RASopathy that is fully explained by a different causative variant. The available evidence is somatic cancer literature and does not document a germline RASopathy phenotype, an alternative causative germline variant, or a VCEP point total. Therefore BP5 cannot be evaluated.
Points are awarded for an alternative molecular cause of a RASopathy in a different gene (and/or in conjunction with BP2) and the phenotype is consistent with expected severity of the RASopathy. Points are also awarded for phenotypes inconsistent with a RASopathy and fully explained by a different causative variant (e.g. WES testing). ... ≥ (-4) Points. ... ≥ (-2) Points. ... ≥ (-1) Point.
PVS1 is not applicable under the BRAF VCEP specification. The VCEP explicitly marks PVS1 as not applicable, and this variant is a missense substitution, NM_004333.6:c.1801A>G (p.Lys601Glu), not a null variant of the types listed in the VCEP's PVS1 description.
Not applicable.
PM3 is not applicable under the ClinGen RASopathy Expert Panel BRAF Version 2.3 CSPEC entry. Therefore, phase, trans/cis observations, affected-proband observations, and inheritance evidence are not used for PM3 in this interpretation.
Not Applicable
PM4 is not applicable to this variant because the VCEP rule names protein-length changes caused by in-frame deletions or insertions in a non-repeat region, or stop-loss variants. NM_004333.6:c.1801A>G produces the missense substitution p.Lys601Glu and does not change protein length or represent a stop-loss event.
Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants. ... No known repetitive areas in gene. Use as described.
The BRAF VCEP explicitly marks PP4 as not applicable and directs evaluation to PS4 instead. No PP4 evidence is used independently.
Not applicable, see PS4.
The BRAF VCEP explicitly states that PP5 is not for use. Literature or ClinVar pathogenic labels therefore cannot be used to apply PP5 under this governing framework.
This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.
The BRAF VCEP CSPEC marks BS3 as Not applicable. The governing approved-functional-studies file likewise assigns BS3_NA for the approved BRAF kinase activity assay, so normal functional results cannot be used to apply BS3 under this VCEP specification.
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
The target is a missense variant, whereas the VCEP's BP1 rule is restricted to truncating variants: nonsense, frameshift, canonical splice-site, initiation-codon, whole-gene, or multi-exon deletions in genes without established loss-of-function correlation.
This rule has contraindications for use with RASopathies. Given the disease mechanism is gain-of-function for RASopathies, BP1 should be used for any truncating variant (nonsense, frameshift, affects canonical splice sites, initiation codon, entire gene or multi exon deletion) in genes without established LOF correlation to disease. See the supplemental material regarding dosage sensitivity information for each individual gene and potential association to disorders associated with LOF variants.
BP3 is explicitly marked not applicable by the BRAF VCEP specification. Its defined use concerns in-frame deletions or insertions in a repetitive region without a known function, whereas this variant is a missense substitution, p.Lys601Glu.
No known benign repetitive areas in RASopathy genes.
The BRAF VCEP explicitly states that BP6 is not for use. A reputable-source benign assertion cannot be converted into BP6 under this framework.
This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.
The variant is missense (NP_004324.2:p.(Lys601Glu)), whereas the governing BRAF VCEP BP7 rule covers synonymous variants and, additionally, intronic positions except canonical splice sites or non-coding variants. This missense variant is outside BP7's stated scope, so BP7 is not applicable without evaluating splice or conservation evidence.
A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved. This rule is also applicable for intronic positions (except canonical splice sites) or non-coding variants and should be used in conjunction with BP4.
Every interpreted variant in BRAF, mapped onto the exon structure of NM_004333.6. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
| Ashkenazi Jewish1 / 29,572 | 3.4e-05 |
| European (non-Finnish)1 / 113,630 | 8.8e-06 |
This variant is present in gnomAD v4.1 (AF= 6.20007e-07; MAF= 0.00006%, 1/1612884 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 3.38158e-05; MAF= 0.00338%, 1/29572 alleles, homozygotes = 0).
This variant is present in gnomAD v2.1 (AF= 3.98004e-06; MAF= 0.00040%, 1/251254 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.80049e-06; MAF= 0.00088%, 1/113630 alleles, homozygotes = 0).
Not available in gnomAD-Canada v1.0.
This is a missense variant, NP_004324.2:p.(Lys601Glu). The governing BRAF VCEP rule specifies the missense PP3 path as REVEL ≥0.7; the REVEL lookup reports 0.916, so PP3 is met at Supporting strength. The available SpliceAI result is not used for this missense PP3 path because the governing rule names REVEL for missense variants, and the same prediction is not counted again under BP4 or BP7.
For missense variants: REVEL ≥ 0.7. For splicing impact, predicted outcome must match disease mechanism.
This is a missense variant, so the governing BRAF VCEP missense BP4 path applies and names REVEL with a cutoff of ≤0.3. The REVEL lookup reports 0.916, which exceeds that cutoff; therefore BP4 is not met. SpliceAI is not substituted for the VCEP's named missense predictor and is not double-counted with PP3.
For missense variants: REVEL ≤0.3.
The variant is missense (NP_004324.2:p.(Lys601Glu)), whereas the governing BRAF VCEP BP7 rule covers synonymous variants and, additionally, intronic positions except canonical splice sites or non-coding variants. This missense variant is outside BP7's stated scope, so BP7 is not applicable without evaluating splice or conservation evidence.
A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved. This rule is also applicable for intronic positions (except canonical splice sites) or non-coding variants and should be used in conjunction with BP4.
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.08). REVEL score = 0.916. BayesDel score = 0.34622.
8 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata.
Thus, activation of RAF by ATP-competitive inhibitors can be explained by transactivation: binding of drug to one RAF in the dimer activates the other.
Results, paragraph beginning "Thus, activation of RAF by ATP-competitive inhibitors..."
Among the three patients with non-V600 or complex BRAF mutations, PFS was 1·5 (K601E), 1·8 (V600_K601E), and 4·2 months (K601E), and no responses were observed.
Results, Tumour Response; Discussion
one case each of a guanine-to-thymine (G–T) transversion at nucleotide 1,382 (R461I), a T–G transversion at nucleotide 1,385 (I462S), a G–A transition at nucleotide 1,388 (G463E), and an A–G transition at nucleotide 1,798 (K600E).
Results, paragraph describing BRAF mutations; Table 1, BRAF mutants
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
This variant is present in gnomAD v4.1 (AF= 6.20007e-07; MAF= 0.00006%, 1/1612884 alleles, homozygotes = 0) and has highest observed frequency in the Ashkenazi Jewish population (AF= 3.38158e-05; MAF= 0.00338%, 1/29572 alleles, homozygotes = 0).
This variant is present in gnomAD v2.1 (AF= 3.98004e-06; MAF= 0.00040%, 1/251254 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.80049e-06; MAF= 0.00088%, 1/113630 alleles, homozygotes = 0).
Not available in gnomAD-Canada v1.0.
This variant has been reported in ClinVar as Likely pathogenic (1 clinical laboratory) and as Pathogenic (1 clinical laboratory). (ClinVarID = 13966)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.08). REVEL score = 0.916. BayesDel score = 0.34622.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Oncogenic.
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV56058494, n = 208 times).
This variant lies in a statistically significant hotspot.