APBA2 p.Gln408=
c.1224A>G · rs140018484 · VCV3052721
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.368%, afr)
Conditions
1
APBA2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.22 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.75 | GERP -3.1 |
| Overall | ||
| CADD | 6.367 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.368%
African / African-American · 276/75,054 alleles
Filtering AF
0.332%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.318%
Overall
0.0185%
299/1,614,198 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.368% | 272 |
| Remaining individualsnot grpmax-eligible | 0.0272% | 3,677 |
| Admixed American | 0.00833% | 12,005 |
| European (non-Finnish) | 8.47e-05% | 1,180,034 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- APBA2
- Protein
- p.Gln408=
- Coding
- c.1224A>G
- MANE Select
- NM_001353788
- dbSNP
- rs140018484
- Type
- single nucleotide variant
- Location
- chr15:29094286 (GRCh38)
- Gene constraint
- LOEUF 0.524 · pLI 0.78 (gnomAD)
- Structure
- AlphaFold pLDDT 59.74
- Residue 408
- the pid domain
Disease context
APBA2-related disorder
Similar variants
- APBA2 c.1070-9C>T Likely benign same condition
- APBA2 c.952-3825C>T Likely benign same condition
- APBA2 c.*7C>T Likely benign same condition
- APBA2 p.Arg52Gln Benign same condition
- APBA2 p.Asn704= Likely benign same condition
- APBA2 p.Asn722Ser Likely benign same condition
- APBA2 p.Asp162= Likely benign same condition
- APBA2 p.Gly603= Benign same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/apba2-p-gln408 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown