NM_002107.4:c.83A>T

H3-3A · NP_002098.1:p.(Lys28Met) · NM_002107.4

GRCh37: chr1:226252135 A>T · GRCh38: chr1:226064434 A>T

Gene: H3-3A Transcript: NM_002107.4

Final call

VUS

PM2 supporting

Variant details

Gene

H3-3A

Transcript

NM_002107.4

Protein

NP_002098.1:p.(Lys28Met)

gnomAD AF

ClinVar

Tier I - Strong

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

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.

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	Not met	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.	pvs1_generic_framework pvs1_variant_assessment pvs1_gene_context
PS1	Not met	No evidence was identified of a previously established pathogenic variant with the same amino acid change (Lys28Met) at this position.
PS2	Not met	No de novo occurrence data with confirmed maternity and paternity is available for this variant.
PS3	Not met	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.	oncokb PMID:23539183 PMID:23603901 PMID:33049227 PMID:22286061
PS4	Not met	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.	clinvar PMID:22918138 PMID:27984673
PS5	Not met	No variant-specific de novo report (with or without confirmed parentage) was identified for K28M.
PM1	Not met	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.
PM2	Met	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.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	No same-residue comparator variants with an established pathogenic classification were identified; automatic PM5 candidate harvesting found zero candidates.	pm5_candidates
PM6	Not met	No de novo observation (without confirmed parentage) has been reported for this variant.
PP1	Not met	No co-segregation data with disease in multiple affected family members is available.
PP2	Not met	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.
PP3	Not met	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.	revel bayesdel spliceai
PP4	Not met	No patient phenotype or family history data are available for this case to assess disease specificity.
PP5	Not met	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.	clinvar PMID:23539183 PMID:22286061 PMID:23603901 PMID:27984673 PMID:22918138
BA1	Not met	The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada. Allele frequency is 0%, far below the BA1 threshold of >1%.	gnomad_v2 gnomad_v4
BS1	Not met	The variant is absent from population databases (AF = 0%), below the BS1 threshold of >0.3%.	gnomad_v2 gnomad_v4
BS2	Not met	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.
BS3	Not met	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.	PMID:23539183 PMID:23603901
BS4	Not met	No segregation data in affected family members are available to assess lack of co-segregation.
BP1	Not met	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.
BP2	Not met	No data are available on observation of this variant in trans with a pathogenic variant for a fully penetrant recessive disorder.
BP4	Not met	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.	revel bayesdel spliceai
BP5	Not met	No data are available showing this variant in a case with an alternate molecular basis for disease.
BP6	Not met	ClinVar classifies this variant as 'Tier I - Strong' (pathogenic-leaning), not benign. No reputable source reports it as benign.	clinvar
BP7	N/A	This is a missense variant (c.83A>T, p.Lys28Met), not a synonymous variant. BP7 is for synonymous variants with no predicted splice impact.

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