The BCL2 NM_000633.3:c.302G>T (NP_000624.2:p.(Gly101Val)) missense variant has not previously been reported in somatic cancers (COSMIC). Experimental evidence: Independent biochemical, structural, cell-line, and patient-cell assays showed approximately 180-fold reduced venetoclax affinity for BCL2 Gly101Val. 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.BCL2 encodes a protein on the outer membrane of mitochondria that helps cells survive by blocking programmed cell death. Abnormally high BCL2 activity is strongly associated with follicular lymphoma and is also seen in other blood cancers, where it can help malignant cells evade death. BCL2 is therefore an important cancer-promoting gene, particularly in hematologic malignancies.
The recorded framework is Generic ACMG/AMP 2015 with ClinGen SVI recommendations. 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 at supporting: independent biochemical, structural, cell-line, and patient-cell assays showed approximately 180-fold reduced venetoclax affinity for BCL2 Gly101Val.
Met at supporting strength: the variant is absent from gnomAD v2.1 and v4.1, below the <=0.0001 PM2 threshold.
No benign criterion marked as applied in the recorded assessment.
VUS: PS3 supporting plus PM2 supporting are the only applied criteria; two supporting criteria do not satisfy a generic ACMG pathogenic or benign rule.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1 allele counts were not recorded for this variant.
Absent from gnomAD v2.1.
Not available in gnomAD-Canada v1.0.
Recorded REVEL score: 0.492. Refer to the recorded PP3/BP4 rationale for interpretation.
A ClinVar laboratory submission summary was not recorded.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.
ACMG/AMP criteria under Generic ACMG/AMP 2015 with ClinGen SVI recommendations, with the data and sources behind each one.
28 criteria with recorded statuses: 2 met · 9 not met · 13 not assessed · 4 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Only the requested codon, residue, domain, and gene-mechanism criteria were adjudicated.
PM1 was not assessed because structural evidence supports a drug-binding region, but critical germline-domain status and absence of benign variation across the region were not established.
PS1 was not met because the same amino-acid change was reported for acquired treatment resistance rather than as a previously established pathogenic variant; PM5, PP2, and BP1 lacked the required gene- or comparator-level evidence.
No VCEP covers BCL2 in this case; the generic ACMG/AMP 2015 definitions govern.
The two full-text variant-specific papers were reviewed for PS4, PP4, and BP5; both concern acquired venetoclax resistance in CLL rather than a germline phenotype case-control comparison, a phenotype-specific diagnosis, or an alternate molecular basis for this case.
PP5 and BP6 were restricted to exact-variant ClinVar expert-panel classifications; ClinVar returned no exact-variant record.
Both criteria are evaluated on the missense REVEL path only under the supplied generic rules; REVEL 0.492 is neither deleterious nor tolerated at the supplied supporting thresholds.
No criteria match.
PS3 is met at supporting strength. Two independent, variant-specific studies evaluated BCL2 Gly101Val (NM_000633.3:c.302G>T; p.Gly101Val) using complementary functional approaches. PMID:30514704 reports reduced venetoclax sensitivity in primary patient CLL cells and engineered cell lines, approximately 180-fold reduced venetoclax binding in surface plasmon resonance assays, impaired venetoclax-mediated displacement of BAX and BAK, and a selective growth advantage during venetoclax exposure. PMID:31160589 independently reports structural and surface-plasmon-resonance evidence that G101V reduces venetoclax affinity from 0.018 nM for wild-type BCL-2 to 3.2 nM, approximately 180-fold, while largely preserving binding to BIM and BAX BH3 peptides; the E152A double mutant largely restored affinity, providing a mechanistic control. These concordant biochemical, structural, cellular, and patient-cell results support an altered damaging drug-response function for the BCL2 gene product. The evidence is not calibrated above supporting because the provided records do not establish reproducibility and robustness in a clinical diagnostic laboratory setting, and the assays primarily establish venetoclax resistance rather than a general disease mechanism.
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.
PM2 is met at supporting strength. NM_000633.3:c.302G>T (BCL2 p.Gly101Val) is absent from gnomAD v2.1 and gnomAD v4.1, with separate reported absence from the gnomAD v2.1 and v3.1 non-cancer subsets. The variant is therefore below the supplied generic PM2 supporting threshold of <=0.0001.
Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
The variant is BCL2 p.Gly101Val (c.302G>T). The two directly relevant publications report this same amino-acid change as an acquired venetoclax-resistance mutation in treated CLL, not as a previously established pathogenic variant. ClinVar has no record for the queried variant, so the evidence does not satisfy PS1's requirement for a previously established pathogenic same-amino-acid variant.
Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. ... Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.
The governing ACMG/AMP PS4 definition requires a significantly increased prevalence in affected individuals compared with controls; its note specifies OR or RR >5.0 with a confidence interval excluding 1.0. The two variant-specific papers report acquired BCL2 Gly101Val in venetoclax-treated CLL patients with treatment resistance or progression, not a germline disease case-control study establishing phenotype prevalence. PMID:30514704 reports 7 patients with the mutation at progression and no mutation at paired treatment entry, plus absence in 96 venetoclax-naive CLL patients and 301 patients with other B-cell malignancies; these treatment cohorts do not provide a validated affected-versus-unaffected case-control comparison for a BCL2-associated germline disease, and no OR/RR with a qualifying confidence interval can be established for the PS4 disease context. Therefore PS4 is not met.
The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0.
The variant is a missense substitution, so the governing generic rule selects the REVEL path only; SpliceAI is not used for PP3 in this situation. REVEL is 0.492, below the generic PP3 supporting threshold of >= 0.644, so PP3 is not met. BayesDel is not used because no generic ACMG-strength calibration is established for it. The threshold is the supplied ClinGen SVI REVEL calibration from Pejaver et al. 2022 (PMID:36413997).
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.).
PP5 requires a reputable source to recently report the variant as pathogenic when the evidence is unavailable for independent evaluation. The exact-variant ClinVar search found no record, no expert-panel classification, and no pathogenic or likely pathogenic expert-panel assertion. The OncoKB label is Likely Oncogenic and cites functional oncology papers, but it is not an exact-variant ClinVar expert-panel classification and cannot trigger PP5 under the specified generic rule. Therefore PP5 is not met.
Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.
BA1 is not met. NM_000633.3:c.302G>T (BCL2 p.Gly101Val) is absent from gnomAD v2.1 and gnomAD v4.1, with corroborating absence in the reported non-cancer subsets. No filtering allele frequency or grpmax FAF is reported, so there is no evidence that the allele frequency reaches the generic stand-alone threshold of >=0.05. The absence of a frequency also avoids a threshold artifact from a small ancestry-specific popmax point estimate.
Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.
BS1 is not met. The variant is absent from gnomAD v2.1 and v4.1, with corroborating absence in the reported non-cancer subsets, so no filtering allele frequency or grpmax FAF exceeds the supplied generic default of >=0.01. Because no elevated frequency is present, a maximum-credible-allele-frequency calculation based on prevalence, penetrance, and allelic heterogeneity is not triggered.
Allele frequency is greater than expected for the disorder.
BS3 is not met. The available variant-specific functional studies do not show no damaging effect on protein function or splicing; instead, they consistently show altered BCL2 function in the venetoclax-response context, including approximately 180-fold reduced venetoclax affinity, reduced drug sensitivity, impaired displacement of pro-apoptotic BAX and BAK, and acquired resistance. No well-established benign functional or splicing result for Gly101Val was identified in the reviewed evidence.
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
The variant is a missense substitution, so the governing generic rule selects the REVEL path only; the SpliceAI result cannot substitute for a gray-zone REVEL result. REVEL is 0.492, which is above the generic BP4 supporting cutoff of <= 0.29 and therefore does not support BP4. BayesDel is not used because no generic ACMG-strength calibration is established for it. The threshold is the supplied ClinGen SVI REVEL calibration from Pejaver et al. 2022 (PMID:36413997).
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc)
BP6 requires a reputable source to recently report the variant as benign when the evidence is unavailable for independent evaluation. The exact-variant ClinVar search found no record, no expert-panel classification, and no benign or likely benign expert-panel assertion. The available OncoKB result is Likely Oncogenic rather than benign and is not an eligible ClinVar expert-panel assertion. Therefore BP6 is not met.
Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.
Not assessed: the available case evidence does not provide a proband disease description, documented absence of family history, or parental testing establishing both maternity and paternity. Therefore, the required evidence for a confirmed de novo occurrence cannot be evaluated.
BCL2 p.Gly101Val lies in the structurally characterized venetoclax-binding pocket of BCL-2. PMID:31160589 directly evaluated the G101V structural change in the P2 pocket and showed approximately 180-fold reduced venetoclax affinity; PMID:30514704 independently demonstrated the same residue's functional effect in patient cells and engineered cell lines. However, the available evidence does not establish that this drug-binding pocket is a critical germline disease domain or demonstrate absence of benign variation across the relevant region. The variant's absence from gnomAD v2.1 and v4.1 alone is insufficient for the full generic PM1 requirement.
Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.
No germline affected-proband, parental/offspring testing, phase information, or pathogenic allele in trans was identified for NM_000633.3:c.302G>T (BCL2 p.Gly101Val). The available variant-specific publications describe an acquired somatic mutation in venetoclax-treated CLL, not a germline recessive disorder or a tested trans configuration. Therefore, PM3 cannot be assessed under the required recessive-disorder rule.
PM3: For recessive disorders, detected in trans with a pathogenic variant...Note: This requires testing of parents (or offspring) to determine phase.
The available case evidence does not document a different missense substitution at BCL2 residue Gly101 that was determined to be pathogenic. The two extracted papers concern the queried Gly101Val substitution itself and do not establish a pathogenic alternate missense comparator at the same residue. A verified same-residue pathogenic comparator is therefore missing.
Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before. ... Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.
Not assessed: the available case evidence does not document an assumed de novo variant in a patient with the disease, nor does it provide parental testing information showing that maternity and paternity were unconfirmed. The criterion cannot be evaluated without a proband and family-testing record.
Not assessed: no affected relatives, family pedigree, variant testing results, or meioses are documented. Consequently, co-segregation with disease in multiple affected family members cannot be evaluated.
The case evidence establishes that the variant is missense, but it does not establish both gene-level requirements for PP2: a low rate of benign missense variation and missense variants as a common mechanism of disease for BCL2. Absence of this single variant from gnomAD is insufficient to establish either gene-level condition.
Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
No patient phenotype or family-history description for the case is provided in the available evidence. The two available variant-specific publications concern acquired venetoclax resistance in CLL and do not establish that this case has a phenotype highly specific for a disease with a single genetic etiology. The criterion cannot be assessed without case-level phenotype and family-history information.
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.
BS2 is not assessed. The available evidence reports population-database absence but does not document this variant in a healthy adult as a heterozygote, homozygote, or hemizygote. It also does not establish that full penetrance is expected at an early age for the relevant BCL2 disorder, so the BS2 observation requirement cannot be evaluated.
Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.
Not assessed: no affected relatives with documented absence of the variant are identified, and no family segregation data are available. Lack of segregation therefore cannot be distinguished from missing family information or phenocopy-related findings.
The variant is missense, but the available evidence does not establish that BCL2 is a gene for which primarily truncating variants are known to cause disease. No sufficiently documented disease-variant spectrum or established gene-level truncating predominance is supplied for this generic assessment.
Missense variant in a gene for which primarily truncating variants are known to cause disease.
No germline observation documents NM_000633.3:c.302G>T (BCL2 p.Gly101Val) in trans with a pathogenic variant in a fully penetrant dominant disorder or in cis with a pathogenic variant. The available variant-specific publications describe an acquired somatic mutation in venetoclax-treated CLL, which does not provide the required germline allelic relationship. Therefore, BP2 cannot be assessed.
BP2: Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.
BP5 requires the variant to be found in a case with an alternate molecular basis for disease. The available case evidence does not provide a case-level diagnosis with an independently established alternate molecular cause. The papers describe acquired resistance during venetoclax treatment, but do not document an alternate molecular basis for the disease in this case. BP5 cannot be assessed from the available evidence.
Variant found in a case with an alternate molecular basis for disease.
PVS1 (ClinGen SVI PVS1 recommendations, PMC6185798, pvs1_generic_framework) applies only to null variant classes — nonsense, frameshift, canonical ±1/2 splice-consensus, translation-initiation-codon loss, and stop-loss variants — each expected to trigger nonsense-mediated decay or otherwise abolish normal protein function. NM_000633.3:c.302G>T in BCL2 is a missense substitution predicted to produce NP_000624.2:p.(Gly101Val). As a result, no null-variant mechanism (nonsense-mediated decay, truncation, or canonical splice disruption) is triggered by this variant class, so PVS1's structural prerequisite is not met by this variant class. No VCEP criteria specification covers PVS1 for BCL2, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_null_variant_class
PM4 (Richards et al. 2015, PMID:25741868) applies to protein length changes: in-frame insertions/deletions in a non-repetitive region, or stop-loss variants that extend the protein past the reference stop codon. NM_000633.3:c.302G>T in BCL2 is a missense substitution predicted to produce NP_000624.2:p.(Gly101Val). As a result, no change in protein length occurs, so there is nothing for this criterion to evaluate, so PM4's structural prerequisite is not met by this variant class. No VCEP criteria specification covers PM4 for BCL2, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_stop_loss_or_nonrepeat_indel
BP3 (Richards et al. 2015, PMID:25741868) applies to in-frame insertions/deletions located in a repetitive region without a known function. NM_000633.3:c.302G>T in BCL2 is a missense substitution predicted to produce NP_000624.2:p.(Gly101Val). As a result, the variant does not alter protein length within a repeat region, so there is nothing for this criterion to evaluate, so BP3's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP3 for BCL2, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_repeat_region_indel
BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_000633.3:c.302G>T in BCL2 is a missense substitution predicted to produce NP_000624.2:p.(Gly101Val). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP7 for BCL2, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_synonymous
Every interpreted variant in BCL2, mapped onto the exon structure of NM_000633.3. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
Absent from gnomAD v4.1.
Absent from gnomAD v2.1.
Not available in gnomAD-Canada v1.0.
The variant is a missense substitution, so the governing generic rule selects the REVEL path only; SpliceAI is not used for PP3 in this situation. REVEL is 0.492, below the generic PP3 supporting threshold of >= 0.644, so PP3 is not met. BayesDel is not used because no generic ACMG-strength calibration is established for it. The threshold is the supplied ClinGen SVI REVEL calibration from Pejaver et al. 2022 (PMID:36413997).
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.).
The variant is a missense substitution, so the governing generic rule selects the REVEL path only; the SpliceAI result cannot substitute for a gray-zone REVEL result. REVEL is 0.492, which is above the generic BP4 supporting cutoff of <= 0.29 and therefore does not support BP4. BayesDel is not used because no generic ACMG-strength calibration is established for it. The threshold is the supplied ClinGen SVI REVEL calibration from Pejaver et al. 2022 (PMID:36413997).
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc)
BP7 (Richards et al. 2015, PMID:25741868) is defined for a synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence and the nucleotide is not highly conserved. NM_000633.3:c.302G>T in BCL2 is a missense substitution predicted to produce NP_000624.2:p.(Gly101Val). As a result, the encoded protein sequence is altered, so the criterion's silent-variant premise does not hold regardless of any splicing prediction, so BP7's structural prerequisite is not met by this variant class. No VCEP criteria specification covers BP7 for BCL2, so the generic ACMG/AMP 2015 definition applies. This determination was made deterministically from the variant's consequence class, prior to LLM adjudication.
deterministic_prefilter: requires_synonymous
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.492. BayesDel score = 0.0732744.
2 paper records listed. 2 cited in the classification.
The novel Gly101Val mutation in BCL2 was identified at progression in seven patients, but not at study entry. It was first detectable after 19-42 months of therapy, and its emergence anticipated clinical disease progression by many months. Gly101Val reduces the affinity of BCL2 for venetoclax by ~180-fold in surface plasmon resonance assays, thereby preventing the drug from displacing pro-apoptotic mediators from BCL2 in cells and conferring acquired resistance in cell lines and primary patient cells.
Location Abstract; Results, sections on genomic assessment of patient samples and functional characterization; Discussion
Context Paired pre-venetoclax and progression samples from patients with relapsed CLL; targeted amplicon sequencing, digital droplet PCR, RNA sequencing, engineered human B-lineage cell lines, cell-viability and cytotoxicity assays, surface plasmon resonance, co-immunoprecipitation, and competition cultures under venetoclax exposure.
This mutant, G101V, was found in chronic lymphocytic leukaemia (CLL) patients from the clinical trials who had initially responded to treatment but developed CLL-type clinical progression after 19-42 months.
Location Introduction, paragraph describing the clinically identified G101V mutation; Results, ‘Structures of BCL-2 mutants bound to venetoclax’; Table 2; ‘The role of E152 in venetoclax affinity’
Context Clinical observations in venetoclax-treated CLL patients; X-ray crystallography of wild-type, G101V, G101A, and other BCL-2 complexes; surface plasmon resonance competition assays for venetoclax and BH3-peptide binding; mutational analysis of the G101V/E152A double mutant.
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.
Absent from gnomAD v4.1.
Absent from gnomAD v2.1.
Not available in gnomAD-Canada v1.0.
This variant is absent from ClinVar.
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.492. BayesDel score = 0.0732744.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
This variant does not lie in a statistically significant hotspot.