APOC2 p.Gln21=
c.63G>A · rs768288162 · VCV1753315
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0267%, amr)
Conditions
1
Cardiovascular phenotype
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 1.2 | GERP -0.56, phastCons 0.95 |
| Overall | ||
| CADD | 4.665 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0267%
Admixed American · 16/59,990 alleles
Filtering AF
0.0166%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0136%
Overall
0.000991%
16/1,613,920 alleles · ultra-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
- APOC2
- Protein
- p.Gln21=
- Coding
- c.63G>A
- MANE Select
- NM_000483
- dbSNP
- rs768288162
- Type
- single nucleotide variant
- Location
- chr19:44948708 (GRCh38)
- Gene constraint
- LOEUF 1.054 · pLI 0.07 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 65.81 · 4 PDB
Similar variants
- APOC2 p.Gln25Ter Likely pathogenic ★★ same condition
- APOC2 p.Ala54Asp Uncertain significance ★★ ⚠ same condition
- APOC2 p.Ala55Thr Uncertain significance ★★ ⚠ same condition
- APOC2 p.Ser76Ile Uncertain significance ★★ ⚠ same condition
- APOC2 p.Thr23Ile Uncertain significance ★★ ⚠ same condition
- APOC2 p.Thr86Arg Uncertain significance ★★ ⚠ same condition
- APOC2 p.Val67Ile Uncertain significance ★★ ⚠ same condition
- APOC2 c.56-4G>C Benign ★★ 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/apoc2-p-gln21 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown