AP3D1 p.Pro697=
c.2091G>A · rs772525867 · VCV2170140
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0657%, mid)
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 -20 | GERP -2.8 |
| Overall | ||
| CADD | 0.005 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0657%
Middle Eastern · 4/6,084 alleles
Filtering AF
0.0224%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0135%
Overall
0.00192%
31/1,612,772 alleles · ultra-rare
exomes 29/1,460,598 · genomes 2/152,174 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0657% | 1,521 |
| African / African-American | 0.016% | 6,242 |
| Remaining individualsnot grpmax-eligible | 0.00801% | 12,491 |
| South Asian | 0.0022% | 45,543 |
| Admixed American | 0.00167% | 59,984 |
| European (non-Finnish) | 0.000593% | 168,524 |
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
- AP3D1
- Protein
- p.Pro697=
- Coding
- c.2091G>A
- MANE Select
- NM_001261826
- dbSNP
- rs772525867
- Type
- single nucleotide variant
- Location
- chr19:2115596 (GRCh38)
- Gene constraint
- LOEUF 0.443 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.45 · 6 PDB
Similar variants
- AP3D1 p.Pro697Leu Uncertain significance ★★ ⚠ same residue
- AP3D1 p.Pro697Thr Uncertain significance ★ ⚠ same residue
- AP3D1 c.2001+6C>T Uncertain significance ★★ same type
- AP3D1 c.2601+6G>T Uncertain significance ★★ same type
- AP3D1 c.856+3G>A Uncertain significance ★★ same type
- AP3D1 p.Ala1076Val Uncertain significance ★★ ⚠ same type
- AP3D1 p.Ala1093Val Uncertain significance ★★ ⚠ same type
- AP3D1 p.Ala1148Val 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/ap3d1-p-pro697 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown