Is ABCD1 p.Glu471= (c.1413A>G) pathogenic?

ABCD1 p.Glu471= (c.1413A>G) is classified Likely benign in ABCD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-12). Very rare (popmax 0.00433%, amr); Associated with adrenoleukodystrophy.

What condition is associated with ABCD1 p.Glu471= (c.1413A>G)?

ABCD1 p.Glu471= (c.1413A>G) is associated with adrenoleukodystrophy (ClinVar).

How common is ABCD1 p.Glu471= (c.1413A>G) in the general population?

ABCD1 p.Glu471= (c.1413A>G) is very rare (popmax 0.00433%, amr) (gnomAD).

How is X-linked adrenoleukodystrophy inherited?

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

ABCD1 p.Glu471=

c.1413A>G · rs782035584 · VCV1139629

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00433%, amr)

Conditions

adrenoleukodystrophy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.04	moderately benign-leaning
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.076	GERP -3.1, phastCons 0.52
Overall
CADD	5.077	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00433% Admixed American · 2/46,176 alleles

Filtering AF 0.000718% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000269%

Overall 0.000273% 3/1,097,627 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00433%	23,088
Remaining individualsnot grpmax-eligible	0.0021%	47,655

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.Glu471=
Coding: c.1413A>G
dbSNP: rs782035584
Type: single nucleotide variant
Location: chrX:153737176 (GRCh38)

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)

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-glu471 (accessed [today's date]).

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