AP3D1 p.Ser634=
c.1902C>T · rs201354946 · VCV742005
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.255%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.58 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.5 | GERP -3.1 |
| Overall | ||
| CADD | 1.189 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.255%
African / African-American · 191/75,024 alleles
Filtering AF
0.225%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.214%
Overall
0.0164%
265/1,611,458 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.255% | 393 |
| Admixed American | 0.0251% | 3,987 |
| Remaining individualsnot grpmax-eligible | 0.00962% | 10,398 |
| European (non-Finnish) | 0.00433% | 23,119 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00339% | 29,516 |
| East Asian | 0.00223% | 44,828 |
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.Ser634=
- Coding
- c.1902C>T
- MANE Select
- NM_001261826
- dbSNP
- rs201354946
- Type
- single nucleotide variant
- Location
- chr19:2116704 (GRCh38)
- Gene constraint
- LOEUF 0.443 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.45 · 6 PDB
- Residue 634
- the 'disordered' region; a modified residue (phosphoserine)
Similar variants
- 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
- AP3D1 p.Ala1213Thr Uncertain significance ★★ ⚠ same type
- AP3D1 p.Ala247Val 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-ser634 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown