AP2S1 p.Lys18=
c.54G>A · VCV3655954
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 1.3 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 11.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- AP2S1
- Protein
- p.Lys18=
- Coding
- c.54G>A
- MANE Select
- NM_004069
- Type
- single nucleotide variant
- Location
- chr19:46846092 (GRCh38)
- Gene constraint
- LOEUF 0.478 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 97.03 · 1 PDB
- Residue 18
- a β-strand
Similar variants
- AP2S1 p.Arg15Cys Pathogenic ★★ same type
- AP2S1 p.Arg15His Pathogenic/Likely pathogenic ★★ same type
- AP2S1 p.Arg15Leu Pathogenic ★★ same type
- AP2S1 c.153+5C>T Uncertain significance ★★ same type
- AP2S1 p.Arg60His Uncertain significance ★★ ⚠ same type
- AP2S1 p.Gln22His Uncertain significance ★★ ⚠ same type
- AP2S1 p.Ile84Val Uncertain significance ★★ ⚠ same type
- AP2S1 p.Thr112Met 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/ap2s1-p-lys18 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown