AP1S2 p.Gln2Ter
c.4C>T · VCV4075752
Likely pathogenic
No assertion criteria
Classification
Likely pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
X-linked syndromic intellectual disability
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 2 of 6 |
| Splicing | ||
| SpliceAI | Δ0.31 | acceptor loss · deltas |
| Pangolin | Δ0.49 | gain · loss 0.15 · SpliceAI calls loss · independent |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 40.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
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
- AP1S2
- Protein
- p.Gln2Ter
- Coding
- c.4C>T
- MANE Select
- NM_001272071
- Type
- single nucleotide variant
- Location
- chrX:15852521 (GRCh38)
- Structure
- AlphaFold pLDDT 94.36
Similar variants
- 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
- AP1S2 p.Leu54Val 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-gln2ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown