APBA2 p.Asn704=
c.2112C>T · rs569262973 · VCV3049085
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.105%, sas)
Conditions
1
APBA2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.1 | GERP -3.4 |
| Overall | ||
| CADD | 8.305 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.105%
South Asian · 96/91,084 alleles
Filtering AF
0.0883%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0819%
Overall
0.0135%
218/1,613,626 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.105% | 949 |
| Remaining individualsnot grpmax-eligible | 0.0304% | 3,289 |
| East Asian | 0.0111% | 8,972 |
| African / African-American | 0.0107% | 9,382 |
| European (non-Finnish) | 0.00712% | 14,048 |
| Admixed American | 0.00666% | 15,006 |
| Finnishnot grpmax-eligible | 0.00315% | 31,744 |
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.Asn704=
- Coding
- c.2112C>T
- MANE Select
- NM_001353788
- dbSNP
- rs569262973
- Type
- single nucleotide variant
- Location
- chr15:29113950 (GRCh38)
- Gene constraint
- LOEUF 0.524 · pLI 0.78 (gnomAD)
- Structure
- AlphaFold pLDDT 59.74
- Residue 704
- the pdz 2 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.Asn722Ser Likely benign same condition
- APBA2 p.Asp162= Likely benign same condition
- APBA2 p.Gln408= 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-asn704 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown