The H3-3A NM_002107.7:c.83A>T (NP_002098.1:p.(Lys28Met)) missense variant has not previously been reported in somatic cancers (COSMIC). 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.H3-3A encodes histone H3.3, a replication-independent protein that is incorporated into chromatin and helps regulate DNA packaging, gene activity, and chromosome organization. It is associated with pediatric glioblastoma and diffuse pontine glioma, where it can contribute to tumor development. H3-3A acts as an oncogene in cancer, with alterations linked to increased tumor growth, invasion, and distinct glioblastoma biology.
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 strength: the variant is absent from gnomAD v2.1 and v4.1, meeting the <=0.0001 PM2 threshold.
No benign criterion marked as applied in the recorded assessment.
VUS: PM2 (supporting) is the only applied criterion, and one supporting criterion does not meet a generic ACMG/AMP classification combination 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.
Absent from gnomAD-Canada v1.0.
Recorded REVEL score: 0.371. Refer to the recorded PP3/BP4 rationale for interpretation.
A ClinVar laboratory submission summary was not recorded. ClinVar API review status: criteria provided, single submitter.
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: 1 met · 7 not met · 15 not assessed · 5 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Population data support PM2 at supporting strength because the variant is absent from the available gnomAD datasets.
BA1 and BS1 are not met because no population frequency is observed, and BS2 is not assessable without a documented healthy-adult genotype observation.
No criteria match.
PM2 is met at supporting strength. NM_002107.7:c.83A>T (p.Lys28Met) is absent from gnomAD v2.1 and v4.1 and from the reported non-cancer subsets, satisfying the generic PM2 absence requirement and the supplied 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.
NM_002107.7:c.83A>T is an exonic missense variant producing NP_002098.1:p.(Lys28Met), so the governing generic rule selects the missense REVEL path only; SpliceAI is not used for PP3/BP4 in this situation. REVEL is 0.371, below the generic PP3 supporting threshold of >= 0.644 calibrated by Pejaver et al. 2022 (PMID:36413997), and BayesDel has no established generic ACMG-strength calibration. Therefore PP3 is not met.
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). ... PP3 (supporting): >= 0.644 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
PP5 is not met because no exact-variant ClinVar expert-panel classification was identified. ClinVar variation 4530459 has only single-submitter somatic assertions with review status "criteria provided, single submitter"; the audit reports zero expert-panel submissions. The PP5-indexed PMID:34131312 is a technical-standard paper and does not report this variant as pathogenic.
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_002107.7:c.83A>T (p.Lys28Met) is absent from gnomAD v2.1 and gnomAD v4.1, including the reported non-cancer subsets, so no allele frequency reaches the 5% stand-alone benign threshold.
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 and from the reported non-cancer subsets, so its observed population frequency is not greater than expected for the disorder. No elevated ancestry-specific frequency is present that would require a maximum-credible-frequency adjustment.
Allele frequency is greater than expected for the disorder.
BP1 is not supported because available gene-context evidence describes H3-3A missense variants as causes of a neurodevelopmental disorder, with reported effects that are gain-of-function or dominant-negative. This is inconsistent with a gene for which primarily truncating variants are known to cause disease. The evidence does not establish a primarily truncating disease mechanism for H3-3A.
Missense variant in a gene for which primarily truncating variants are known to cause disease.
NM_002107.7:c.83A>T is an exonic missense variant producing NP_002098.1:p.(Lys28Met), so the governing generic rule selects the missense REVEL path only; the low SpliceAI score cannot substitute for a non-supportive missense REVEL result. REVEL is 0.371, above the generic BP4 supporting threshold of <= 0.29 calibrated by Pejaver et al. 2022 (PMID:36413997). BayesDel has no established generic ACMG-strength calibration. Therefore BP4 is not met.
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc). ... BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
BP6 is not met because no exact-variant ClinVar expert-panel classification as benign or likely benign was identified. ClinVar variation 4530459 has zero expert-panel submissions and only single-submitter somatic assertions; no reputable expert-panel benign assertion is available.
Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.
The variant is NM_002107.7:c.83A>T, p.Lys28Met. The reviewed evidence does not establish a previously established pathogenic variant producing the same Lys28Met amino-acid change through a different nucleotide change. The available literature concerns different substitutions, principally H3F3A/H3.3 K27M, and the ClinVar record is a somatic single-submitter record without extracted criterion-level evidence. A verified pathogenic same-amino-acid comparator is required before PS1 can be adjudicated.
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.
No proband-level de novo evidence is available. The case materials do not document a patient with the relevant disease, absence of family history, or confirmed maternity and paternity; therefore PS2 cannot be assessed.
De novo (both maternity and paternity confirmed) in a patient with the disease and no family history. ... Confirmation of paternity only is insufficient.
No validated, reproducible functional assay directly evaluating NM_002107.7:c.83A>T (NP_002098.1:p.(Lys28Met)) was identified. The reviewed functional publications studied different substitutions, including H3F3A/H3.3 K27M and yeast histone H3 Lys42Ala, and therefore cannot establish a damaging effect for this variant. Variant-specific functional evidence sufficient to apply PS3 is absent.
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.
No case-control study or affected-versus-unaffected/population count comparison for the exact variant NM_002107.7:c.83A>T (NP_002098.1:p.Lys28Met) was identified. The literature packet's PS4-indexed PMID:34131312 is a chromosomal-microarray technical standard whose abstract does not mention this variant or provide case/control counts. Therefore, an OR and 95% CI cannot be computed, and the ACMG PS4 threshold cannot be evaluated.
The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... Note 1: 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 at H3-3A residue Lys28. No VCEP covers H3-3A and vcep_materials.json contains no domain table. The reviewed hotspot evidence identifies H3F3A K27M, not residue K28, and the case hotspot search found no statistically significant H3-3A K28 hotspot. The available evidence does not establish that Lys28 lies in a critical and well-established functional domain without benign variation, so PM1 cannot be adjudicated from the supplied evidence.
Located in a mutational hot spot and/or critical and well-established functional domain (e.g. active site of an enzyme) without benign variation.
The variant is p.Lys28Met. No different missense substitution at residue Lys28 has been verified as pathogenic in the supplied evidence. The collected comparator artifact contains zero same-residue candidates, while the reviewed papers concern other residues, especially K27. A verified pathogenic alternate missense change at Lys28 is required before PM5 can be adjudicated.
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.
No evidence documents an assumed de novo occurrence. The case materials do not report parental testing, parental variant status, or a clinical context supporting de novo inference; therefore PM6 cannot be assessed.
Assumed de novo, but without confirmation of paternity and maternity.
No family-based segregation data are available. The case materials do not identify multiple affected family members carrying the variant or provide meioses or cosegregation counts; therefore PP1 cannot be assessed.
Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease. ... May be used as stronger evidence with increasing segregation data.
H3-3A missense disease mechanism is described in the available gene-context literature, but the supplied evidence does not establish the separate PP2 requirement that the gene has a low rate of benign missense variation. No quantified or otherwise validated benign-missense-rate assessment for H3-3A is available. The absent population observation for this individual variant cannot substitute for a gene-level benign missense rate.
Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.
The available case evidence identifies the variant and its molecular consequence but does not provide an individual patient phenotype, family history, or a defined disease presentation that can be judged highly specific for a single genetic etiology. The PP4 requirement therefore cannot be evaluated.
Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.
BS2 cannot be assessed from the available evidence. No observation is provided of this variant in a healthy adult individual, and population absence cannot establish the required healthy-adult genotype observation or the required full-penetrance early-onset disease context.
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.
No well-established functional study directly evaluating NM_002107.7:c.83A>T (NP_002098.1:p.(Lys28Met)) demonstrated absence of a damaging effect on protein function or splicing. The reviewed studies concerned different histone H3 substitutions and cannot provide variant-specific benign functional evidence for p.Lys28Met. Variant-specific functional evidence sufficient to apply BS3 is absent.
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
No affected family members or family testing results are documented. Consequently, lack of segregation cannot be evaluated, and BS4 cannot be assessed.
Lack of segregation in affected members of a family.
BP2 cannot be assessed because the available evidence does not document a pathogenic variant in trans in a fully penetrant dominant disorder or a pathogenic variant in cis in any inheritance pattern; no affected-proband phase data are provided.
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.
No patient-level case report or clinical record was available showing this exact variant in a case with an alternate molecular basis for the disease. The available somatic ClinVar conditions and unrelated literature references do not establish that BP5's case-level alternate molecular-basis requirement is satisfied.
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_002107.7:c.83A>T in H3-3A is a missense substitution predicted to produce NP_002098.1:p.(Lys28Met). 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 H3-3A, 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
PM3 is not applicable because its governing definition is limited to recessive disorders, whereas the available case evidence does not establish a recessive H3-3A disorder context; no phase or pathogenic-variant-in-trans observation is available either.
For recessive disorders, detected in trans with a pathogenic variant
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_002107.7:c.83A>T in H3-3A is a missense substitution predicted to produce NP_002098.1:p.(Lys28Met). 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 H3-3A, 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_002107.7:c.83A>T in H3-3A is a missense substitution predicted to produce NP_002098.1:p.(Lys28Met). 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 H3-3A, 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_002107.7:c.83A>T in H3-3A is a missense substitution predicted to produce NP_002098.1:p.(Lys28Met). 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 H3-3A, 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 H3-3A, mapped onto the exon structure of NM_002107.7. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
Absent from gnomAD v4.1.
Absent from gnomAD v2.1.
Absent from gnomAD-Canada v1.0.
NM_002107.7:c.83A>T is an exonic missense variant producing NP_002098.1:p.(Lys28Met), so the governing generic rule selects the missense REVEL path only; SpliceAI is not used for PP3/BP4 in this situation. REVEL is 0.371, below the generic PP3 supporting threshold of >= 0.644 calibrated by Pejaver et al. 2022 (PMID:36413997), and BayesDel has no established generic ACMG-strength calibration. Therefore PP3 is not met.
Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.). ... PP3 (supporting): >= 0.644 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
NM_002107.7:c.83A>T is an exonic missense variant producing NP_002098.1:p.(Lys28Met), so the governing generic rule selects the missense REVEL path only; the low SpliceAI score cannot substitute for a non-supportive missense REVEL result. REVEL is 0.371, above the generic BP4 supporting threshold of <= 0.29 calibrated by Pejaver et al. 2022 (PMID:36413997). BayesDel has no established generic ACMG-strength calibration. Therefore BP4 is not met.
Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc). ... BP4 (supporting): <= 0.29 — ClinGen SVI REVEL calibration (Pejaver et al. 2022, Am J Hum Genet) (PMID:36413997)
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_002107.7:c.83A>T in H3-3A is a missense substitution predicted to produce NP_002098.1:p.(Lys28Met). 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 H3-3A, 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 = 0.04). REVEL score = 0.371. BayesDel score = -0.120005.
9 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.
Here we describe in vivo consequences of eliminating a single protein–DNA interaction at this position through mutagenesis of histone H3 Lys 42 to alanine.
Abstract
Recent studies have identified a Lys 27-to-methionine (K27M) mutation at one allele of H3F3A, one of the two genes encoding histone H3 variant H3.3, in 60% of high-grade pediatric glioma cases.
Abstract; Results and Discussion, sections describing H3.3K27M patient-derived DIPG cells and ectopic-expression assays
H3F3A K27M High-grade pontine glioma (26) Pilocytic astrocytoma (1) Brain 27 2.2 × 10−50
Results, Table 2, Organ system-specific hotspots
About 80% of DMGs contain the recurrent histone H3 lysine 27 (H3 K27M) mutation in genes encoding histone H3 proteins
Introduction, paragraph 1; Results, section ‘H3 K27M Interacts with PRC2 In vivo and Impedes Its Spreading’
We demonstrate that this is caused by aberrant recruitment of the PRC2 complex to K27M mutant H3.3 and enzymatic inhibition of the H3K27me3-establishing methyltransferase EZH2.
Summary; Introduction; Results sections on H3K27me3 reduction and K27M mutant H3.3 activity
In our pLGG series, all H3F3A mutations were p.K27M, with no p.G34R/V alterations identified
Results, ‘H3.3 p.K27M’ subsection; Figure 6D; Figure 7 risk stratification
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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.
Absent from gnomAD-Canada v1.0.
This variant has been reported in ClinVar but submission details could not be extracted. (ClinVarID = 4530459)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04). REVEL score = 0.371. BayesDel score = -0.120005.
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.