Is ABCD1 p.Arg259Gln (c.776G>A) pathogenic?

ABCD1 p.Arg259Gln (c.776G>A) is classified Uncertain significance in ABCD1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2024-08-28). AlphaMissense: likely benign (0.2119); Very rare (popmax 0.00723%, sas); Associated with adrenoleukodystrophy.

What condition is associated with ABCD1 p.Arg259Gln (c.776G>A)?

ABCD1 p.Arg259Gln (c.776G>A) is associated with adrenoleukodystrophy (ClinVar).

How common is ABCD1 p.Arg259Gln (c.776G>A) in the general population?

ABCD1 p.Arg259Gln (c.776G>A) is very rare (popmax 0.00723%, sas) (gnomAD).

How is X-linked adrenoleukodystrophy inherited?

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

What do computational predictors say about ABCD1 p.Arg259Gln (c.776G>A)?

AlphaMissense predicts likely benign (score 0.2119) — an in-silico prediction, not a clinical call.

ABCD1 p.Arg259Gln

c.776G>A · rs200191405 · VCV1210518

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

likely benign

0.2119 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00723%, sas)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

adrenoleukodystrophy

Computational evidence

Protein change
AlphaMissense	0.2119	likely benign
REVEL	0.827	moderately pathogenic-leaning
SaProt	LLR -10.49	damaging
⇒ REVEL and SaProt call this damaging; AlphaMissense does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.7	GERP 0.75, phastCons 1
Regional constraint	o/e 0.94	unconstrained · MANE · 865 bp · p 0.3 · regional, not allelic
Overall
CADD	25.1	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00723% South Asian · 4/55,296 alleles

Filtering AF 0.00512% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00468%

Overall 0.00551% 66/1,198,552 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00723%	13,824
European (non-Finnish)	0.00653%	15,319
Remaining individualsnot grpmax-eligible	0.00638%	15,682
East Asian	0.00299%	33,389

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: ABCD1
Protein: p.Arg259Gln
Coding: c.776G>A
MANE Select: NM_000033
dbSNP: rs200191405
Type: single nucleotide variant
Location: chrX:153726042 (GRCh38)
Structure: AlphaFold pLDDT 81.58 · 14 PDB
Residue 259: an α-helix; the abc transmembrane type-1 domain

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.Arg259Trp Uncertain significance ★★ ⚠ same residue
ABCD1 p.Arg259Pro Uncertain significance ★ ⚠ same residue
ABCD1 c.1635-2A>G Pathogenic ★★ same condition
ABCD1 c.1781-1G>C Pathogenic ★★ same condition
ABCD1 c.1781-1G>T Pathogenic/Likely pathogenic ★★ same condition
ABCD1 c.1866-10G>A Pathogenic/Likely pathogenic ★★ same condition
ABCD1 c.1866-1G>C Likely pathogenic ★★ same condition
ABCD1 c.1866-2A>T 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-arg259gln (accessed [today's date]).

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