ABCA1 p.Arg437=
c.1311G>A · VCV3609468
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0133%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.61 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.44 | gain · loss 0.13 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 4 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 24.7 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0133%
African / African-American · 10/74,992 alleles
Filtering AF
0.00722%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00549%
Overall
0.00062%
10/1,612,446 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
- ABCA1
- Protein
- p.Arg437=
- Coding
- c.1311G>A
- MANE Select
- NM_005502
- Type
- single nucleotide variant
- Location
- chr9:104836980 (GRCh38)
- Gene constraint
- LOEUF 0.563 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.50 · 7 PDB
- Residue 437
- an α-helix
Similar variants
- ABCA1 p.Arg437Leu Uncertain significance ★ same residue
- ABCA1 c.4175+1G>T Pathogenic/Likely pathogenic ★★ same type
- ABCA1 c.4274+1G>A Likely pathogenic ★★ same type
- ABCA1 c.5237+3A>C Likely pathogenic ★★ same type
- ABCA1 p.Arg2080Trp Likely pathogenic ★★ same type
- ABCA1 p.Arg557Ter Pathogenic/Likely pathogenic ★★ same type
- ABCA1 p.Arg587Trp Pathogenic/Likely pathogenic ★★ same type
- ABCA1 p.Asn1800His Pathogenic/Likely 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/abca1-p-arg437 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown