APBA2 p.Leu629=
c.1885C>T · rs76687371 · VCV786259
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.65%, afr)
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 5.9 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 12.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.65%
African / African-American · 2,738/75,020 alleles
Filtering AF
3.54%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.49%
Overall
0.192%
3,092/1,612,928 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.65% | 27 |
| Remaining individualsnot grpmax-eligible | 0.302% | 331 |
| Admixed American | 0.213% | 469 |
| Middle Eastern | 0.116% | 866 |
| South Asian | 0.00549% | 18,216 |
| European (non-Finnish) | 0.00212% | 47,196 |
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.Leu629=
- Coding
- c.1885C>T
- MANE Select
- NM_001353788
- dbSNP
- rs76687371
- Type
- single nucleotide variant
- Location
- chr15:29106787 (GRCh38)
- Gene constraint
- LOEUF 0.524 · pLI 0.78 (gnomAD)
- Structure
- AlphaFold pLDDT 59.74
- Residue 629
- the pdz 1 domain
Similar variants
- APBA2 p.Val77Met Uncertain significance ★★ ⚠ same type
- APBA2 c.1216-9T>C Benign ★★ same type
- APBA2 c.1525-8C>G Likely benign ★★ same type
- APBA2 c.1705-9C>T Benign ★★ same type
- APBA2 p.Asp87= Benign ★★ same type
- APBA2 p.Gly206= Benign ★★ same type
- APBA2 p.His127= Benign ★★ same type
- APBA2 p.Ile101= Benign ★★ same type
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-leu629 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown