APOA1 p.Leu202=
c.606T>C · VCV4827119
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,608,040)
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 -2.7 |
| Overall | ||
| CADD | 7.696 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,608,040). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- APOA1
- Protein
- p.Leu202=
- Coding
- c.606T>C
- MANE Select
- NM_000039
- Type
- single nucleotide variant
- Location
- chr11:116836006 (GRCh38)
- Gene constraint
- LOEUF 1.168 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.66 · 31 PDB
- Residue 202
- the '10 x approximate tandem repeats' region; a UniProt-annotated variant site (in fha2; no protein expression); a UniProt-annotated variant site (in hdl deficiency; with periorbital xanthelasmas; decreased protein abundance); a UniProt-annotated variant site (in fha2; missing protein expression); an α-helix
Similar variants
- APOA1 p.Leu202Pro Pathogenic same residue
- APOA1 p.Ala176Thr Uncertain significance ★★ ⚠ same condition
- APOA1 p.Ala176Val Uncertain significance ★★ ⚠ same condition
- APOA1 p.Ala204Val Uncertain significance ★★ ⚠ same condition
- APOA1 p.Ala218Thr Uncertain significance ★★ ⚠ same condition
- APOA1 p.Ala256Thr Uncertain significance ★★ ⚠ same condition
- APOA1 p.Arg140Leu Uncertain significance ★★ ⚠ same condition
- APOA1 p.Arg175Gly Uncertain significance ★★ ⚠ 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/apoa1-p-leu202 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown