Is ACSL4 p.Asp503= (c.1509T>C) pathogenic?

ACSL4 p.Asp503= (c.1509T>C) is classified Likely benign in ACSL4 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-10-01). Ultra-rare (popmax 0.0482%, amr); Associated with Inborn genetic diseases.

What condition is associated with ACSL4 p.Asp503= (c.1509T>C)?

ACSL4 p.Asp503= (c.1509T>C) is associated with Inborn genetic diseases (ClinVar).

How common is ACSL4 p.Asp503= (c.1509T>C) in the general population?

ACSL4 p.Asp503= (c.1509T>C) is ultra-rare (popmax 0.0482%, amr) (gnomAD).

ACSL4 p.Asp503=

c.1509T>C · rs772803365 · VCV589504

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0482%, amr)

Conditions

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 5.4	GERP 1.9, phastCons 1
Overall
CADD	10.15	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0482% Admixed American · 22/45,690 alleles

Filtering AF 0.0326% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0275%

Overall 0.00182% 22/1,207,761 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: ACSL4
Protein: p.Asp503=
Coding: c.1509T>C
MANE Select: NM_001318510
dbSNP: rs772803365
Type: single nucleotide variant
Location: chrX:109663284 (GRCh38)
Structure: AlphaFold pLDDT 90.46

Full ACSL4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ACSL4 p.Asp503Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
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

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-asp503 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown