APOC2 p.Leu11=
c.33T>C · rs1392234344 · VCV1959024
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 -4.9 | GERP -2 |
| Overall | ||
| CADD | 0.149 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,860 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000274%
4/1,461,860 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,860 |
| European (non-Finnish) | 0.000254% | 393,334 |
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.Leu11=
- Coding
- c.33T>C
- MANE Select
- NM_000483
- dbSNP
- rs1392234344
- Type
- single nucleotide variant
- Location
- chr19:44948511 (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 type
- APOC2 p.Gln92Ter Pathogenic/Likely pathogenic ★★ same type
- APOC2 p.Ala54Asp Uncertain significance ★★ ⚠ same type
- APOC2 p.Ala55Thr Uncertain significance ★★ ⚠ same type
- APOC2 p.Ser76Ile Uncertain significance ★★ ⚠ same type
- APOC2 p.Thr23Ile Uncertain significance ★★ ⚠ same type
- APOC2 p.Thr86Arg Uncertain significance ★★ ⚠ same type
- APOC2 p.Val67Ile 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/apoc2-p-leu11 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown