AP3D1 p.Phe138=
c.414C>T · rs770510212 · VCV2733079
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.012%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.52 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.22 | gain · loss 0.04 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 2.5 | GERP -2.3, phastCons 1 |
| Overall | ||
| CADD | 18.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.012%
European (non-Finnish) · 141/1,177,854 alleles
Filtering AF
0.0103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00974%
Overall
0.00912%
147/1,611,374 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.012% | 8,354 |
| Remaining individualsnot grpmax-eligible | 0.00963% | 10,389 |
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.Phe138=
- Coding
- c.414C>T
- MANE Select
- NM_001261826
- dbSNP
- rs770510212
- Type
- single nucleotide variant
- Location
- chr19:2132519 (GRCh38)
- Gene constraint
- LOEUF 0.443 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.45 · 6 PDB
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-phe138 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown