ABCA3 p.Pro248=
c.744G>A · rs149353430 · VCV2968293
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0264%, sas)
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 -14 | GERP -3.7 |
| Overall | ||
| CADD | 0.402 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0264%
South Asian · 24/91,070 alleles
Filtering AF
0.0181%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0154%
Overall
0.00248%
40/1,613,572 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0264% | 3,795 |
| African / African-American | 0.00534% | 18,715 |
| East Asian | 0.00223% | 44,880 |
| Admixed American | 0.00167% | 59,966 |
| European (non-Finnish) | 0.000847% | 118,000 |
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
- ABCA3
- Protein
- p.Pro248=
- Coding
- c.744G>A
- MANE Select
- NM_001089
- dbSNP
- rs149353430
- Type
- single nucleotide variant
- Location
- chr16:2319710 (GRCh38)
- Gene constraint
- LOEUF 0.612 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.00 · 2 PDB
Similar variants
- ABCA3 p.Pro248Leu Pathogenic/Likely pathogenic ★★ same residue
- ABCA3 p.Pro248Ser Likely pathogenic ★ same residue
- ABCA3 c.1112-20G>A Likely pathogenic ★★ same type
- ABCA3 c.2053-1G>C Likely pathogenic ★★ same type
- ABCA3 c.2414+1G>A Likely pathogenic ★★ same type
- ABCA3 c.3863-98C>T Pathogenic ★★ same type
- ABCA3 c.614-2A>G Likely pathogenic ★★ same type
- ABCA3 p.Ala1070Thr 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/abca3-p-pro248 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown