APOA1 p.Trp22Ter
c.66G>A · VCV3619394
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 |
|---|---|---|
| NMD | predicted | premature termination codon in exon 3 of 4 |
| Splicing | ||
| SpliceAI | Δ0.33 | acceptor gain · deltas |
| Constraint at this position | ||
| Conservation | phyloP 4.9 | GERP 2.4, phastCons 1 |
| Overall | ||
| CADD | 41.0 | 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
- APOA1
- Protein
- p.Trp22Ter
- Coding
- c.66G>A
- MANE Select
- NM_000039
- Type
- single nucleotide variant
- Location
- chr11:116837135 (GRCh38)
- Gene constraint
- LOEUF 1.168 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.66 · 31 PDB
Similar variants
- APOA1 p.Arg197Pro Pathogenic ★★ same type
- APOA1 p.Gln23Ter Pathogenic ★★ same type
- APOA1 p.Gly50Arg Pathogenic ★★ same type
- APOA1 c.-21+22G>A Uncertain significance ★★ same type
- APOA1 p.Ala176Thr Uncertain significance ★★ ⚠ same type
- APOA1 p.Ala176Val Uncertain significance ★★ ⚠ same type
- APOA1 p.Ala204Val Uncertain significance ★★ ⚠ same type
- APOA1 p.Ala218Thr 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/apoa1-p-trp22ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown