ABCA12 p.Leu474=
c.1422C>T · rs142374853 · VCV2884680
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.015%, amr)
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 -7.3 | GERP -4.7 |
| Overall | ||
| CADD | 0.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.015%
Admixed American · 9/60,000 alleles
Filtering AF
0.00952%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00896%
Overall
0.00929%
150/1,614,058 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.015% | 6,667 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,930 |
| European (non-Finnish) | 0.0111% | 9,008 |
| East Asian | 0.00223% | 44,864 |
| African / African-American | 0.00133% | 75,016 |
| South Asian | 0.0011% | 91,074 |
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
- ABCA12
- Protein
- p.Leu474=
- Coding
- c.1422C>T
- MANE Select
- NM_173076
- dbSNP
- rs142374853
- Type
- single nucleotide variant
- Location
- chr2:215019662 (GRCh38)
- Gene constraint
- LOEUF 0.582 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.32
- Residue 474
- a UniProt-annotated variant site (in arci4b)
Similar variants
- ABCA12 p.Leu474Phe Uncertain significance ★ ⚠ same residue
- ABCA12 c.2592+1G>A Likely pathogenic ★★ same type
- ABCA12 c.5381+1G>C Pathogenic/Likely pathogenic ★★ same type
- ABCA12 c.985+1G>A Likely pathogenic ★★ same type
- ABCA12 p.Arg1297Ter Pathogenic ★★ same type
- ABCA12 p.Arg1514Cys Pathogenic ★★ same type
- ABCA12 p.Arg1514His Pathogenic/Likely pathogenic ★★ same type
- ABCA12 p.Arg1515Ter Pathogenic ★★ 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/abca12-p-leu474 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown