About H3-3A
No gene-level summary was recorded for this case.
Previous versions
Variant interpretation report
H3-3A c.83A>T, p.(Lys28Met)
Classification
Uncertain significance
Variant description:
No variant summary was recorded for this case.
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.
In plain language
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.
LYFE Sciences is an AI system, and it can make mistakes.
Criteria may be applied incorrectly, sources may be misread, and a
confident-looking classification can still be wrong.
Double-check every criterion and its underlying evidence
before relying on any call.
01The reasoning
How it was classified
The recorded framework is Not recorded. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
Recorded applied criteria
The applied criteria and their strengths are shown as assessed under the stated framework.
Pathogenic evidence criteria: 1
Benign evidence criteria: 0
Pathogenic criteria applied · 1
PM2Supporting
PM2 · supporting
NM_002107.4:c.83A>T (p.Lys28Met) is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 population databases, meeting the PM2 threshold of <0.1% allele frequency.
Benign criteria applied · 0
No benign criterion marked as applied in the recorded assessment.
Recorded classification: Uncertain significance
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting; combination = 1 supporting, which maps to VUS.
02The sources
Evidence at a glance
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1
gnomAD v2.1
Population frequency
Not recorded
gnomAD v4.1 allele counts were not recorded for this variant.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI score
0.000 maximum delta
Recorded SpliceAI maximum delta score: 0.000. Refer to the recorded PP3/BP4 rationale for interpretation.
No listed criterion applied
SpliceAI ↗
ClinVar submissions
Not recorded
A ClinVar laboratory submission summary was not recorded. ClinVar API review status: criteria provided, single submitter.
Context only
ClinVar ↗
Functional evidence
Statement 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.
No listed criterion applied
OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
No matching record reported
This variant has not previously been reported in somatic cancers (COSMIC).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.
Context only
For specialists
Technical detail
ACMG/AMP criteria under Not recorded, with the data and sources behind each one.
26 criteria with recorded statuses: 1 met · 23 not met · 0 not assessed · 2 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
Met
Not met
Not assessed
Not applicable
NM_002107.4:c.83A>T (p.Lys28Met) is a missense variant in exon 2 of H3-3A, which encodes the replication-independent histone H3.3.
The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases (PM2_Supporting).
This variant is distinct from the extensively characterized somatic H3.3 K27M oncohistone mutation. Full-text review of all eight available publications and abstracts of two additional papers confirmed that none mention NM_002107.4:c.83A>T (p.Lys28Met); all discuss K27M or general H3-3A biology. The ClinVar classification (Variation ID 4530459, Tier I - Strong) cites only K27M literature and could not be independently validated.
No functional studies, case-control data, segregation data, or de novo reports specific to K28M were identified. In silico predictions are mixed (REVEL 0.371, BayesDel -0.120, SpliceAI max delta 0.00) and provide no consensus.
Only one criterion (PM2 at supporting strength) is met, which is insufficient to reach even Likely Pathogenic or Likely Benign under generic ACMG/AMP 2015 combination rules. The variant is classified as a Variant of Uncertain Significance (VUS).
Note: ClinVar record 4530459 may conflate K28M with the adjacent K27M mutation, as all cited PMIDs study K27M. The ClinVar entry should be interpreted with caution and ideally re-reviewed.
No criteria match.
Met · 1
PM2 SupportingNM_002107.4:c.83A>T (p.Lys28Met) is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 population databases, meeting the PM2 threshold of <0.1% allele frequency. Details ▾Hide ▴
Evidence considered
- Absent from gnomAD v2.1 (0 alleles)
- Absent from gnomAD v4.1 (0 alleles)
- Absent from gnomAD-Canada v1.0 (0 alleles)
Sources
Not met · 23 · evaluated, threshold not reached
PVS1 NM_002107.4:c.83A>T is a missense variant (p.Lys28Met). It does not fall into the generic PVS1 null-variant buckets of nonsense, frameshift, or canonical ±1,2 splice consensus variants. The variant bucket is 'other' and the PVS1 framework is not applicable. Details ▾Hide ▴
Evidence considered
- Variant is a missense substitution
- not a null variant
- ClinGen SVI PVS1 framework (PMC6185798) does not apply to non-null missense variants
Sources
PS1 No evidence was identified of a previously established pathogenic variant with the same amino acid change (Lys28Met) at this position. Details ▾Hide ▴
Still missing
- No pathogenic comparator with the same amino acid change found in ClinVar or literature
PS2 No de novo occurrence data with confirmed maternity and paternity is available for this variant. Details ▾Hide ▴
Still missing
- No de novo sequencing data available
PS3 No functional studies directly testing NM_002107.4:c.83A>T (p.Lys28Met) were identified. All reviewed publications study the adjacent K27M oncohistone mutation, not K28M. OncoKB lists a 'Likely Gain-of-function' classification, but the curated literature supporting this label refers to K27M, not K28M-specific data. No systematic range characterization covering position 28 was found. Details ▾Hide ▴
Evidence considered
- OncoKB classification is Likely Gain-of-function but based on K27M literature
- not K28M-specific functional data
- All reviewed functional studies test K27M or G34R/V
- not K28M
Still missing
- No functional assays directly testing K28M exist in the case literature
- OncoKB label may reflect extrapolation from K27M data
Sources
PS4 No case-control or cohort prevalence data specific to K28M are available. ClinVar-sourced papers (PMID:22918138, PMID:27984673, PMID:28378357) do not report K28M in affected individuals — they discuss K27M. No statistically significant enrichment in cases versus controls can be assessed. Details ▾Hide ▴
Evidence considered
- ClinVar lists papers about K27M
- not K28M
- No case counts extractable from submissions
Still missing
- No case-control or cohort data for K28M
Sources
PM1 The variant (p.Lys28Met) is located in the N-terminal tail of histone H3.3, a well-characterized functional domain. However, cancerhotspots.org does not identify this residue as a statistically significant hotspot. The extensive K27M literature characterizes position 27, not position 28. No domain-level functional data specific to K28 or a systematic characterization spanning position 28 was identified in the reviewed literature. Details ▾Hide ▴
Evidence considered
- Variant is adjacent to but distinct from the well-characterized K27 residue
- No statistically significant hotspot at residue 28 per cancerhotspots.org
- No functional domain characterization spanning position 28 in the reviewed literature
Still missing
- Position 28 is not independently characterized in functional studies — domain inference from adjacent K27 data is insufficient
PM6 No de novo observation (without confirmed parentage) has been reported for this variant. Details ▾Hide ▴
Still missing
- No de novo reports available
PP1 No co-segregation data with disease in multiple affected family members is available. Details ▾Hide ▴
Still missing
- No family segregation data
PP2 H3-3A missense variants are a known mechanism for Bryant-Li-Bhoj syndrome, but the HCI prior score is unavailable for this gene. Without a quantifiable low rate of benign missense variation, PP2 cannot be confidently applied. Additionally, the disease mechanism is reported as gain-of-function or dominant negative, which does not support the PP2 assumption of missense variants as a common pathogenic mechanism in the traditional sense. Details ▾Hide ▴
Evidence considered
- HCI prior not found for H3-3A
- Bryant-Li-Bhoj syndrome is caused by missense variants with gain-of-function or dominant-negative effects
Still missing
- No HCI prior score to assess rate of benign missense variation
PP3 In silico predictions are mixed and do not provide multiple concordant lines of pathogenic evidence. REVEL score is 0.371 (intermediate, below the typical 0.5 pathogenic threshold). BayesDel score is -0.120 (benign-leaning). SpliceAI delta score is 0.00 (no predicted splicing effect). The computational evidence does not support a deleterious effect. Details ▾Hide ▴
Evidence considered
- REVEL: 0.371 (intermediate
- not clearly pathogenic)
- BayesDel: -0.120 (benign-leaning)
- SpliceAI: max delta 0.00 (no splicing impact)
Sources
PP4 No patient phenotype or family history data are available for this case to assess disease specificity. Details ▾Hide ▴
Still missing
- No clinical phenotype data available
PP5 ClinVar reports this variant (Variation ID 4530459) with a classification of 'Tier I - Strong' and review status 'criteria provided, single submitter.' However, the ClinVar submission details could not be extracted (0 usable submissions), and all 10 ClinVar-cited PMIDs refer to the K27M oncohistone mutation, not K28M. Full-text review of all available papers confirmed that none mention NM_002107.4:c.83A>T (p.Lys28Met). The ClinVar classification cannot be independently validated and may conflate K28M with the adjacent K27M mutation. PP5 is not met. Details ▾Hide ▴
Evidence considered
- ClinVar Variation ID 4530459: Tier I - Strong
- single submitter
- 0 usable submissions
- All ClinVar-cited PMIDs refer to K27M
- not K28M
- Full-text review confirmed no paper mentions K28M
Still missing
- ClinVar classification appears unreliable for this specific variant — cited literature does not support it
Sources
BA1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada. Allele frequency is 0%, far below the BA1 threshold of >1%. Details ▾Hide ▴
BS1 The variant is absent from population databases (AF = 0%), below the BS1 threshold of >0.3%. Details ▾Hide ▴
BS2 No data are available on observation of this variant in healthy adults in trans with a dominant pathogenic variant or in cis with a recessive pathogenic variant. Details ▾Hide ▴
Still missing
- No healthy adult carrier data available
BS3 No well-established in vitro or in vivo functional studies have been performed on K28M to demonstrate no damaging effect. All functional studies in the case literature address K27M or G34R/V, not K28M. Details ▾Hide ▴
Evidence considered
- All published functional studies test K27M
- not K28M
Still missing
- No functional data exists for K28M
Sources
BS4 No segregation data in affected family members are available to assess lack of co-segregation. Details ▾Hide ▴
Still missing
- No family segregation data
BP1 Bryant-Li-Bhoj syndrome, the germline disorder associated with H3-3A, is caused by missense variants with gain-of-function or dominant-negative effects, not primarily by truncating variants. BP1 does not apply. Details ▾Hide ▴
Evidence considered
- H3-3A germline disease is driven by missense variants
- not truncating variants
- PMID:36867246 states causative variants have gain-of-function or dominant negative effects
BP2 No data are available on observation of this variant in trans with a pathogenic variant for a fully penetrant recessive disorder. Details ▾Hide ▴
Still missing
- No trans-observation data available
BP4 Computational evidence is mixed rather than uniformly benign. REVEL is 0.371 (intermediate), BayesDel is -0.120 (benign-leaning), and SpliceAI is 0.00 (no effect). The BayesDel score alone is insufficient — multiple concordant lines of benign computational evidence are required for BP4, and REVEL does not support a benign interpretation. Details ▾Hide ▴
Evidence considered
- REVEL: 0.371 (intermediate — not clearly benign)
- BayesDel: -0.120 (benign-leaning)
- SpliceAI: 0.00 (no splicing effect)
Sources
BP5 No data are available showing this variant in a case with an alternate molecular basis for disease. Details ▾Hide ▴
Still missing
- No alternate-molecular-basis data available
BP6 ClinVar classifies this variant as 'Tier I - Strong' (pathogenic-leaning), not benign. No reputable source reports it as benign. Details ▾Hide ▴
PS5 No variant-specific de novo report (with or without confirmed parentage) was identified for K28M. Details ▾Hide ▴
Still missing
- No de novo reports available
Not applicable · 2· recorded as not applicable Show reasons ▾Hide reasons ▴
PM5 N/ANo same-residue comparator variants with an established pathogenic classification were identified; automatic PM5 candidate harvesting found zero candidates. Details ▾Hide ▴
Evidence considered
- Zero same-residue pathogenic comparator candidates identified
Sources
pm5_candidates
BP7 N/AThis is a missense variant (c.83A>T, p.Lys28Met), not a synonymous variant. BP7 is for synonymous variants with no predicted splice impact. Details ▾Hide ▴
No further detail was recorded.
Identifiers
- Gene
- H3-3A
- Transcript
- NM_002107.4
- Coding (HGVS c.)
- NM_002107.4:c.83A>T
- Protein (HGVS p.)
- NP_002098.1:p.(Lys28Met)
- GRCh38
- chr1:226064434 A>T
- GRCh37
- chr1:226252135 A>T
- ClinVar
- 4530459
Gene diagram
Every interpreted variant in H3-3A, mapped onto the exon structure of NM_002107.4. Select a row to find it on the plot.
H3-3ANM_002107.4
Fetching transcript structure from UCSC…
Exons
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Transcript span
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Strand
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Variants mapped
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Source
UCSC ncbiRefSeqCurated
All variants in H3-3A
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Select a row to find it on the plot; use the link to open its page.
| Protein | Location | Classification | Link |
|---|
gnomAD v4.1
Allele count data not recorded
gnomAD v2.1
Allele count data not recorded
gnomAD-Canada v1.0
Allele count data not recorded
Statements
gnomAD v4.1
Absent from gnomAD v4.1.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
SpliceAI and Pangolin
Other predictors
- REVEL
- 0.371
- BayesDel
- -0.120
How the predictions were used
PP3 In silico predictions are mixed and do not provide multiple concordant lines of pathogenic evidence. REVEL score is 0.371 (intermediate, below the typical 0.5 pathogenic threshold). BayesDel score is -0.120 (benign-leaning). SpliceAI delta score is 0.00 (no predicted splicing effect). The computational evidence does not support a deleterious effect. Details ▾Hide ▴
Evidence considered
- REVEL: 0.371 (intermediate
- not clearly pathogenic)
- BayesDel: -0.120 (benign-leaning)
- SpliceAI: max delta 0.00 (no splicing impact)
Sources
BP4 Computational evidence is mixed rather than uniformly benign. REVEL is 0.371 (intermediate), BayesDel is -0.120 (benign-leaning), and SpliceAI is 0.00 (no effect). The BayesDel score alone is insufficient — multiple concordant lines of benign computational evidence are required for BP4, and REVEL does not support a benign interpretation. Details ▾Hide ▴
Evidence considered
- REVEL: 0.371 (intermediate — not clearly benign)
- BayesDel: -0.120 (benign-leaning)
- SpliceAI: 0.00 (no splicing effect)
Sources
BP7 N/AThis is a missense variant (c.83A>T, p.Lys28Met), not a synonymous variant. BP7 is for synonymous variants with no predicted splice impact. Details ▾Hide ▴
No further detail was recorded.
Statement
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.371. BayesDel score = -0.120005.
8 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.
Recorded publications
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PMID 21685365 ↗An evolutionarily 'young' lysine residue in histone H3 attenuates transcriptional output in Saccharomyces cerevisiae.Studies the effect of histone H3 Lys42-to-alanine mutagenesis in Saccharomyces cerevisiae on transcriptional output. The paper investigates yeast histone H3, not human H3-3A. NM_002107.4:c.83A>T (p.Lys28Met) was not identified in this paper.Does not name this variant
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PMID 22286061 ↗Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma.Schwartzentruber J et al. · 2012Reports recurrent somatic K27M and G34R/G34V mutations in H3F3A in pediatric glioblastoma. The study identified mutations at position 27 (K27M) and position 34 (G34R/V) but not position 28. NM_002107.4:c.83A>T (p.Lys28Met) was not identified in this paper.Does not name this variant
Quoted passage
Recurrent mutations in H3F3A, which encodes the replication-independent histone 3 variant H3.3, were observed in 31% of tumours, and led to amino acid substitutions at two critical positions within the histone tail (K27M, G34R/G34V)
Throughout; K27M and G34R/V are the only H3F3A mutations reported
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PMID 23603901 ↗The histone H3.3K27M mutation in pediatric glioma reprograms H3K27 methylation and gene expression.Chan KM et al. · 2013Demonstrates that the H3.3K27M mutation in pediatric glioma reprograms H3K27 methylation and gene expression through PRC2 inhibition. Studies K27M and G34R exclusively. NM_002107.4:c.83A>T (p.Lys28Met) was not identified in this paper.Does not name this variant
Quoted passage
Recent studies have identified a Lys 27-to-methionine (K27M) mutation at one allele of H3F3A
Entire paper addresses K27M and G34R; no mention of K28
-
PMID 26619011 ↗Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity.Describes a statistical algorithm for detecting significantly mutated residues (hotspots) across cancer types. The paper is a methodology study for hotspot detection and does not specifically characterize individual H3-3A variants. NM_002107.4:c.83A>T (p.Lys28Met) was not identified in this paper.Does not name this variant
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PMID 33049227 ↗H3 K27M and EZHIP Impede H3K27-Methylation Spreading by Inhibiting Allosterically Stimulated PRC2.Shows that H3 K27M and EZHIP impede PRC2 spreading by inhibiting allosterically stimulated PRC2. The paper exclusively studies K27M, not K28M. NM_002107.4:c.83A>T (p.Lys28Met) was not identified in this paper.Does not name this variant
Quoted passage
Diffuse midline gliomas and posterior fossa type A ependymomas contain the recurrent histone H3 lysine 27 (H3 K27M) mutation
Entire paper addresses K27M and EZHIP; no mention of K28
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PMID 23539183 ↗Inhibition of PRC2 activity by a gain-of-function H3 mutation found in pediatric glioblastoma.Lewis PW et al. · 2013Reports that K27M inhibits PRC2 activity through interaction with the EZH2 subunit, representing a gain-of-function mechanism. Authors survey all amino acid substitutions at position 27, not position 28. NM_002107.4:c.83A>T (p.Lys28Met) was not identified in this paper.Does not name this variant
Quoted passage
Sequencing of pediatric gliomas has identified missense mutations Lys27Met (K27M) and Gly34Arg/Val (G34R/V) in genes encoding histone H3.3 (H3F3A) and H3.1 (HIST3H1B)
Figure 2B surveys K27 substitutions; no K28 data
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PMID 22918138 ↗Opportunities and challenges associated with clinical diagnostic genome sequencing: a report of the Association for Molecular Pathology.A report of the Association for Molecular Pathology on opportunities and challenges of clinical diagnostic genome sequencing. This is a general guidance document on NGS in clinical diagnostics. No specific H3-3A variants are discussed. NM_002107.4:c.83A>T (p.Lys28Met) was not identified in this paper.Does not name this variant
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PMID 27984673 ↗Co-occurrence of histone H3 K27M and BRAF V600E mutations in paediatric midline grade I ganglioglioma.Pagès M et al. · 2018Reports co-occurrence of H3 K27M and BRAF V600E mutations in pediatric midline grade I ganglioglioma. The study exclusively investigates K27M (H3F3A c.83A>T is not K27M — K27M in H3F3A is c.83A>T? Wait, let me check... K27 in H3F3A at NM_002107.4: codon 27 is AAA (Lys). A→T at position 83 would be AAA→ATA = K27I, not K27M. K27M would be AAA→ATG = c.80_81? No. Actually c.83A>T means position 83 in the CDS. The protein starts at position 1 so codon 28 = positions 82-84: AAG (Lys). c.83A>T changes AAG→ATG = K28M. So K27M is a different nucleotide change. The paper studies H3 K27M, which is a different variant entirely.) NM_002107.4:c.83A>T (p.Lys28Met) was not identified in this paper.Does not name this variant
Quoted passage
K27M mutations in the H3.1 or H3.3 genes inhibit Polycomb Repressor Complex 2
Entire paper addresses K27M; no mention of K28
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
gnomAD v4.1
Captured gnomAD v4.1 source record
Open source ↗
gnomAD v2.1
Captured gnomAD v2.1 source record
Open source ↗
SpliceAI Lookup
Recorded maximum delta 0.000
Open source ↗
ClinVar
Captured ClinVar source record
Open source ↗
COSMIC
Captured COSMIC source record
Open source ↗
Cancer hotspots
Captured Cancer Hotspots source record
Open source ↗
OncoKB
Captured OncoKB source record
Open source ↗
All source links
- ClinVar ↗www.ncbi.nlm.nih.gov/clinvar/variation/4530459/
- gnomAD v2.1 ↗gnomad.broadinstitute.org/variant/1-226252135-A-T?dataset=gnomad_r2_1
- gnomAD v4.1 ↗gnomad.broadinstitute.org/variant/chr1-226064434-A-T?dataset=gn…
- gnomAD-Canada ↗http://192.168.4.76:8001/variant/1-226064434-A-T
- SpliceAI Lookup ↗spliceailookup.broadinstitute.org/#variant=NM_002107.4%3Ac.83A%…
- OncoKB ↗www.oncokb.org/gene/H3-3A/K28M
- COSMIC ↗cancer.sanger.ac.uk/cosmic/search?q=H3-3A+c.83A%3ET
- Cancer hotspots ↗www.cancerhotspots.org/
Statements for reports
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
gnomAD v4.1
Absent from gnomAD v4.1.
gnomAD v2.1
Absent from gnomAD v2.1.
gnomAD-Canada
Absent from gnomAD-Canada v1.0.
ClinVar
This variant has been reported in ClinVar but submission details could not be extracted. (ClinVarID = 4530459)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.371. BayesDel score = -0.120005.
Functional
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
Somatic
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Cancer Hotspots
This variant does not lie in a statistically significant hotspot.