ABCA2 p.Leu853=
c.2559C>T · rs144508979 · VCV2571350
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.53%, mid)
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 -0.14 | GERP -2.4, phastCons 0.33 |
| Overall | ||
| CADD | 5.727 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.53%
Middle Eastern · 93/6,060 alleles
Filtering AF
1.28%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.19%
Overall
0.284%
4,577/1,612,512 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.53% | 65 |
| South Asian | 0.665% | 150 |
| European (non-Finnish) | 0.299% | 335 |
| Remaining individualsnot grpmax-eligible | 0.288% | 347 |
| Admixed American | 0.192% | 522 |
| African / African-American | 0.056% | 1,787 |
| Ashkenazi Jewishnot grpmax-eligible | 0.027% | 3,700 |
| Finnishnot grpmax-eligible | 0.0176% | 5,696 |
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
- ABCA2
- Protein
- p.Leu853=
- Coding
- c.2559C>T
- MANE Select
- NM_001606
- dbSNP
- rs144508979
- Type
- single nucleotide variant
- Location
- chr9:137017119 (GRCh38)
- Gene constraint
- LOEUF 0.436 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 71.46
- Residue 853
- a UniProt-annotated variant site (in idpogsa)
Similar variants
- ABCA2 p.Leu853Phe Uncertain significance ★ ⚠ same residue
- ABCA2 p.Gln1370Ter Likely pathogenic ★★ same type
- ABCA2 c.3883-3C>T Uncertain significance ★★ same type
- ABCA2 p.Ala1357Thr Uncertain significance ★★ ⚠ same type
- ABCA2 p.Ala1620Thr Uncertain significance ★★ ⚠ same type
- ABCA2 p.Ala1645Val Uncertain significance ★★ ⚠ same type
- ABCA2 p.Ala1715Ser Uncertain significance ★★ ⚠ same type
- ABCA2 p.Ala2180Thr 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/abca2-p-leu853 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown