Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.84%, afr)
Conditions
2
autoinflammatory syndrome
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 -1.3 | GERP -4.4 |
| Overall | ||
| CADD | 2.209 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.84%
African / African-American · 3,625/74,842 alleles
Filtering AF
4.71%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.66%
Overall
0.259%
4,175/1,611,866 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.84% | 21 |
| Middle Eastern | 0.611% | 164 |
| Remaining individualsnot grpmax-eligible | 0.335% | 299 |
| Admixed American | 0.266% | 376 |
| South Asian | 0.0198% | 5,042 |
| European (non-Finnish) | 0.0108% | 9,285 |
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
- AP3B1
- Protein
- p.Ala113=
- Coding
- c.339A>C
- MANE Select
- NM_003664
- dbSNP
- rs7706167
- Type
- single nucleotide variant
- Location
- chr5:78228180 (GRCh38)
- Gene constraint
- LOEUF 0.59 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.85 · 5 PDB
Similar variants
- AP3B1 p.Ala113Val Uncertain significance ★ ⚠ same residue
- AP3B1 c.2078-1G>A Likely pathogenic ★★ same condition
- AP3B1 c.280-2A>G Likely pathogenic ★★ same condition
- AP3B1 p.Arg104Ter Pathogenic/Likely pathogenic ★★ same condition
- AP3B1 p.Arg649Ter Pathogenic/Likely pathogenic ★★ same condition
- AP3B1 c.128+4A>G Uncertain significance ★★ same condition
- AP3B1 c.2077+6T>C Uncertain significance ★★ same condition
- AP3B1 c.2809+4A>G Uncertain significance ★★ 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/ap3b1-p-ala113 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown