ACSL4 p.Val596=
c.1788T>C · VCV4566032
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0458%, mid)
Conditions
1
Inborn genetic diseases
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 2.7 | GERP -0.9, phastCons 1 |
| Overall | ||
| CADD | 8.259 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0458%
Middle Eastern · 2/4,367 alleles
Filtering AF
0.0176%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0143%
Overall
0.00174%
21/1,206,525 alleles · ultra-rare
exomes 20/1,095,229 · genomes 1/111,296 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0458% | 2,184 |
| South Asian | 0.0282% | 3,547 |
| European (non-Finnish) | 0.000336% | 297,515 |
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
- ACSL4
- Protein
- p.Val596=
- Coding
- c.1788T>C
- MANE Select
- NM_001318510
- Type
- single nucleotide variant
- Location
- chrX:109659421 (GRCh38)
- Structure
- AlphaFold pLDDT 90.46
Similar variants
- ACSL4 p.Asn95Asp Uncertain significance ★★ ⚠ same condition
- ACSL4 p.Asn95Ser Uncertain significance ★★ ⚠ same condition
- ACSL4 p.His23Arg Uncertain significance ★★ ⚠ same condition
- ACSL4 p.Pro404Leu Uncertain significance ★★ ⚠ same condition
- ACSL4 p.Ser501Tyr Uncertain significance ★★ ⚠ same condition
- ACSL4 p.Tyr132Cys Uncertain significance ★★ ⚠ same condition
- ACSL4 p.Asn153Ser Benign/Likely benign ★★ ⚠ same condition
- ACSL4 p.Asp503= Likely benign ★★ same condition
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/acsl4-p-val596 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown