AP1B1 p.Ala87=
c.261C>T · rs143484030 · VCV3047984
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0801%, nfe)
Conditions
1
AP1B1-related disorder
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 -8.1 | GERP -4.1 |
| Overall | ||
| CADD | 1.27 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0801%
European (non-Finnish) · 945/1,179,828 alleles
Filtering AF
0.0758%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0741%
Overall
0.0634%
1,023/1,613,616 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0801% | 1,248 |
| Remaining individualsnot grpmax-eligible | 0.072% | 1,388 |
| Middle Eastern | 0.0658% | 1,520 |
| Admixed American | 0.035% | 2,856 |
| African / African-American | 0.00934% | 10,704 |
| Finnishnot grpmax-eligible | 0.00156% | 64,032 |
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
- AP1B1
- Protein
- p.Ala87=
- Coding
- c.261C>T
- MANE Select
- NM_001127
- dbSNP
- rs143484030
- Type
- single nucleotide variant
- Location
- chr22:29359842 (GRCh38)
- Gene constraint
- LOEUF 0.476 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 82.46 · 20 PDB
- Residue 87
- a turn
Disease context
AP1B1-related disorder
Similar variants
- AP1B1 p.Gly643Ser Uncertain significance ⚠ same condition
- AP1B1 c.2164-8C>T Likely benign same condition
- AP1B1 c.2309+8C>T Likely benign same condition
- AP1B1 c.2524+5G>A Likely benign same condition
- AP1B1 c.*7G>A Likely benign same condition
- AP1B1 p.Ala373= Likely benign same condition
- AP1B1 p.Ala609= Likely benign same condition
- AP1B1 p.Arg235His Likely benign ⚠ 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/ap1b1-p-ala87 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown