ACSL4 p.Pro520=
c.1560C>T · rs372276636 · VCV588518
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0461%, 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 -1.2 | GERP -3.7 |
| Overall | ||
| CADD | 0.991 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0461%
Middle Eastern · 2/4,338 alleles
Filtering AF
0.00815%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00421%
Overall
0.00507%
61/1,203,413 alleles · ultra-rare
exomes 55/1,091,819 · genomes 6/111,594 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0461% | 2,169 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00916% | 10,921 |
| Remaining individualsnot grpmax-eligible | 0.00633% | 15,787 |
| European (non-Finnish) | 0.00595% | 16,813 |
| African / African-American | 0.00175% | 57,010 |
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.Pro520=
- Coding
- c.1560C>T
- MANE Select
- NM_001318510
- dbSNP
- rs372276636
- Type
- single nucleotide variant
- Location
- chrX:109663233 (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-pro520 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown