Is AP3D1 p.Ala886= (c.2658C>T) pathogenic?

AP3D1 p.Ala886= (c.2658C>T) is classified Likely benign in AP3D1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-29). Very rare (popmax 0.00259%, amr).

How common is AP3D1 p.Ala886= (c.2658C>T) in the general population?

AP3D1 p.Ala886= (c.2658C>T) is very rare (popmax 0.00259%, amr) (gnomAD).

AP3D1 p.Ala886=

c.2658C>T · rs2018342986 · VCV1597234

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00259%, amr)

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 -0.069	GERP -2.9, phastCons 0.009
Overall
CADD	1.281	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00259% Admixed American · 1/38,602 alleles

Filtering AF 0.000269% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000173%

Overall 0.000557% 8/1,435,922 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00259%	38,602
European (non-Finnish)	0.000648%	154,440

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.Ala886=
Coding: c.2658C>T
MANE Select: NM_001261826
dbSNP: rs2018342986
Type: single nucleotide variant
Location: chr19:2113357 (GRCh38)
Gene constraint: LOEUF 0.443 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 76.45 · 6 PDB
Residue 886: the 'disordered' region

Full AP3D1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

AP3D1 p.Ala886Val 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
AP3D1 p.Ala1213Thr 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-ala886 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown