AP3B2 p.Pro645=
c.1935G>A · rs9806343 · VCV1577264
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 11.6%, afr) — too common for a highly-penetrant pathogenic allele
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 -2.8 | GERP -3.8 |
| Overall | ||
| CADD | 6.569 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
11.6%
African / African-American · 8,653/74,622 alleles
Filtering AF
11.4%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 11.3%
Overall
3.72%
59,832/1,610,388 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 11.6% | 9 |
| Admixed American | 8.53% | 12 |
| Finnishnot grpmax-eligible | 5.37% | 19 |
| Middle Eastern | 4.62% | 22 |
| Remaining individualsnot grpmax-eligible | 3.93% | 25 |
| Ashkenazi Jewishnot grpmax-eligible | 3.72% | 27 |
| European (non-Finnish) | 3.08% | 32 |
| South Asian | 2.77% | 36 |
| East Asian | 0.103% | 975 |
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.Pro645=
- Coding
- c.1935G>A
- MANE Select
- NM_001278512
- dbSNP
- rs9806343
- Type
- single nucleotide variant
- Location
- chr15:82665493 (GRCh38)
- Gene constraint
- LOEUF 0.52 · pLI 0.22 (gnomAD)
- Structure
- AlphaFold pLDDT 75.73
Similar variants
- 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
- AP3B2 p.Ala1098Asp 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-pro645 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown