Is ABCD1 p.Arg163del (c.487_489del) pathogenic?

ABCD1 p.Arg163del (c.487489del) is classified Uncertain significance in ABCD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-01). Associated with adrenoleukodystrophy.

What condition is associated with ABCD1 p.Arg163del (c.487_489del)?

ABCD1 p.Arg163del (c.487_489del) is associated with adrenoleukodystrophy (ClinVar).

How is X-linked adrenoleukodystrophy inherited?

Typically X-linked dominant (Orphanet). A genetic counselor can assess individual risk for a family.

ABCD1 p.Arg163del

c.487_489del · VCV4292374

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

Conditions

adrenoleukodystrophy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.9	GERP 1.7, phastCons 1

Variant & gene context

Gene: ABCD1
Protein: p.Arg163del
Coding: c.487_489del
MANE Select: NM_000033
Type: Deletion
Location: chrX:153725752 (GRCh38)
Structure: AlphaFold pLDDT 81.58 · 14 PDB
Residue 163: an α-helix; a UniProt-annotated variant site (in ald); the abc transmembrane type-1 domain; the 'interaction with pex19' region

Full ABCD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

adrenoleukodystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For X-linked adrenoleukodystrophy (Orphanet):

Inheritance: X-linked dominant
Onset: Adolescent, Adult, Childhood, Elderly
Prevalence: 1-9 / 1 000 000 (Israel)

Similar variants

ABCD1 p.Arg163fs Pathogenic ★ same residue
ABCD1 p.Arg163Cys Pathogenic/Likely pathogenic ★★ same residue
ABCD1 p.Arg163Gly Likely pathogenic ★★ same residue
ABCD1 p.Arg163His Pathogenic/Likely pathogenic ★★ same residue
ABCD1 p.Arg163Leu Likely pathogenic ★ same residue
ABCD1 p.Arg163Ser Likely pathogenic ★ same residue
ABCD1 p.Arg163= Likely benign ★ same residue
ABCD1 c.1394-2_1404del Pathogenic/Likely pathogenic ★★ 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/abcd1-p-arg163del (accessed [today's date]).

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