ABCD1 p.Arg163=
c.489C>T · rs2522266000 · VCV2028755
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
adrenoleukodystrophy
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 0.43 | GERP -3.4, phastCons 0.98 |
| Overall | ||
| CADD | 9.745 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ABCD1
- Protein
- p.Arg163=
- Coding
- c.489C>T
- MANE Select
- NM_000033
- dbSNP
- rs2522266000
- Type
- single nucleotide variant
- Location
- chrX:153725755 (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
Disease context
adrenoleukodystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor X-linked adrenoleukodystrophy (Orphanet):
- Inheritance
- X-linked dominant
- Onset
- Adolescent, Adult, Childhood, Elderly
- Prevalence
- 1-9 / 1 000 000 (Israel)
Similar variants
- 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.Arg163fs Pathogenic ★ same residue
- ABCD1 p.Arg163del Uncertain significance ★ same residue
- ABCD1 p.Arg163Pro Pathogenic ★ same residue
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-arg163 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown