AP1S2 c.*1C>T
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0352%, sas)
Conditions
1
Inborn genetic diseases
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 0.58 | GERP -0.2, phastCons 0.99 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 8.528 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0352%
South Asian · 20/56,755 alleles
Filtering AF
0.0233%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0195%
Overall
0.00257%
31/1,205,012 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0352% | 2,838 |
| Middle Eastern | 0.023% | 4,355 |
| Remaining individualsnot grpmax-eligible | 0.00421% | 23,730 |
| East Asian | 0.00296% | 33,757 |
| European (non-Finnish) | 0.000786% | 127,211 |
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
- Coding
- c.*1C>T
- MANE Select
- NM_001272071
- dbSNP
- rs1016898604
- Type
- single nucleotide variant
- Location
- chrX:15827324 (GRCh38)
- Structure
- AlphaFold pLDDT 94.36
Similar variants
- AP1S2 p.Gly158Arg Uncertain significance ★★ ⚠ same condition
- AP1S2 p.Ile134Thr Uncertain significance ★★ ⚠ same condition
- AP1S2 p.Ile82Val Uncertain significance ★★ ⚠ same condition
- AP1S2 p.Leu54Val Uncertain significance ★★ ⚠ same condition
- AP1S2 c.289-8C>T Benign/Likely benign ★★ same condition
- AP1S2 p.Ser96= Benign/Likely benign ★★ same condition
- AP1S2 p.Val38Ile Benign/Likely benign ★★ ⚠ same condition
- AP1S2 p.Ser23Ter Pathogenic ★ 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/ap1s2-c-star-1c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown