ABCA3 p.Phe1592=
c.4776C>T · VCV4775148
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0367%, 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 5.6 | GERP -0.027, phastCons 1 |
| Overall | ||
| CADD | 10.91 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0367%
Admixed American · 22/60,006 alleles
Filtering AF
0.0248%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0209%
Overall
0.00143%
23/1,613,220 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0367% | 2,728 |
| East Asian | 0.00223% | 44,898 |
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.Phe1592=
- Coding
- c.4776C>T
- MANE Select
- NM_001089
- Type
- single nucleotide variant
- Location
- chr16:2278012 (GRCh38)
- Gene constraint
- LOEUF 0.612 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.00 · 2 PDB
- Residue 1592
- the abc transporter 2 domain; a β-strand; a UniProt-annotated variant site (in smdp3)
Similar variants
- ABCA3 p.Phe1592fs 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
- ABCA3 p.Arg1550Trp 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-phe1592 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown