AP2S1 p.Arg53=
c.159G>C · rs899780265 · VCV2847938
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
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 0.73 | GERP 0.62, phastCons 1 |
| Overall | ||
| CADD | 11.21 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,032 alleles
Overall
6.84e-05%
1/1,461,872 alleles · very rare
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
- AP2S1
- Protein
- p.Arg53=
- Coding
- c.159G>C
- MANE Select
- NM_004069
- dbSNP
- rs899780265
- Type
- single nucleotide variant
- Location
- chr19:46839573 (GRCh38)
- Gene constraint
- LOEUF 0.478 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 97.03 · 1 PDB
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-arg53 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown