APBA2 p.Ser73=
c.219C>T · rs151295064 · VCV3051142
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.099%, nfe)
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 1.4 | GERP 0.43, phastCons 1 |
| Overall | ||
| CADD | 9.548 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.099%
European (non-Finnish) · 1,168/1,180,046 alleles
Filtering AF
0.0943%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0923%
Overall
0.0748%
1,207/1,614,054 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.099% | 1,010 |
| Remaining individualsnot grpmax-eligible | 0.0464% | 2,154 |
| Middle Eastern | 0.0165% | 6,052 |
| African / African-American | 0.012% | 8,328 |
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.Ser73=
- Coding
- c.219C>T
- MANE Select
- NM_001353788
- dbSNP
- rs151295064
- Type
- single nucleotide variant
- Location
- chr15:29054103 (GRCh38)
- Gene constraint
- LOEUF 0.524 · pLI 0.78 (gnomAD)
- Structure
- AlphaFold pLDDT 59.74
- Residue 73
- the 'disordered' region
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.Gln408= Likely 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-ser73 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown