AP1S2 p.Leu22=
c.66A>G · VCV3608379
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00691%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.364 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -4.2 | GERP -3.8 |
| Overall | ||
| CADD | 4.348 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00691%
African / African-American · 4/57,894 alleles
Filtering AF
0.00231%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00139%
Overall
0.00137%
15/1,097,368 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00691% | 14,473 |
| Remaining individualsnot grpmax-eligible | 0.0042% | 23,812 |
| European (non-Finnish) | 0.00101% | 99,432 |
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
- AP1S2
- Protein
- p.Leu22=
- Coding
- c.66A>G
- MANE Select
- NM_001272071
- Type
- single nucleotide variant
- Location
- chrX:15852459 (GRCh38)
- Structure
- AlphaFold pLDDT 94.36
Similar variants
- AP1S2 p.Leu22fs Likely pathogenic ★ same residue
- AP1S2 c.-1+1G>A Pathogenic/Likely pathogenic ★★ same type
- AP1S2 p.Arg52Ter Pathogenic ★★ same type
- AP1S2 p.Gln123Ter Pathogenic ★★ same type
- AP1S2 p.Asn129Thr Uncertain significance ★★ ⚠ same type
- AP1S2 p.Gly158Arg Uncertain significance ★★ ⚠ same type
- AP1S2 p.Ile134Thr Uncertain significance ★★ ⚠ same type
- AP1S2 p.Ile82Val 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/ap1s2-p-leu22 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown