AP3B2 p.Ser792=
c.2376C>T · rs766189809 · VCV1530350
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00668%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -8.6 | GERP -3.4 |
| Overall | ||
| CADD | 0.657 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
East Asian · 3/44,882 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00161%
Overall
0.00112%
18/1,613,748 alleles · very rare
exomes 16/1,461,578 · genomes 2/152,170 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00668% | 14,961 |
| African / African-American | 0.00667% | 14,982 |
| South Asian | 0.0011% | 91,070 |
| European (non-Finnish) | 0.000763% | 131,097 |
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
- AP3B2
- Protein
- p.Ser792=
- Coding
- c.2376C>T
- MANE Select
- NM_001278512
- dbSNP
- rs766189809
- Type
- single nucleotide variant
- Location
- chr15:82663861 (GRCh38)
- Gene constraint
- LOEUF 0.52 · pLI 0.22 (gnomAD)
- Structure
- AlphaFold pLDDT 75.73
- Residue 792
- the 'disordered' region
Similar variants
- AP3B2 p.Ser792Phe Uncertain significance ★ ⚠ same residue
- AP3B2 c.114-1G>A Likely pathogenic ★★ same type
- AP3B2 p.Arg977Ter Pathogenic ★★ same type
- AP3B2 p.Gln839Ter Pathogenic/Likely pathogenic ★★ same type
- AP3B2 c.1110+3G>C Uncertain significance ★★ same type
- AP3B2 c.1853-5C>A Uncertain significance ★★ same type
- AP3B2 c.2834-3C>A Uncertain significance ★★ same type
- AP3B2 p.Ala1076Pro Uncertain significance ★★ 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/ap3b2-p-ser792 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown