Is ABCD1 p.Glu609Lys (c.1825G>A) pathogenic?

ABCD1 p.Glu609Lys (c.1825G>A) is classified Pathogenic in ABCD1 (ClinVar, Multiple submitters, 13 submitters; last evaluated 2025-11-28). AlphaMissense: likely pathogenic (0.9856); No allele count reported in gnomAD v4.1 (AN 1,200,842); Associated with ABCD1-related disorder.

What condition is associated with ABCD1 p.Glu609Lys (c.1825G>A)?

ABCD1 p.Glu609Lys (c.1825G>A) is associated with ABCD1-related disorder, adrenoleukodystrophy (ClinVar).

How common is ABCD1 p.Glu609Lys (c.1825G>A) in the general population?

ABCD1 p.Glu609Lys (c.1825G>A) is no allele count reported in gnomAD v4.1 (AN 1,200,842) (gnomAD).

What do computational predictors say about ABCD1 p.Glu609Lys (c.1825G>A)?

AlphaMissense predicts likely pathogenic (score 0.9856) — an in-silico prediction, not a clinical call.

ABCD1 p.Glu609Lys

c.1825G>A · rs150346282 · VCV166626

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 13 submitters

AlphaMissense

likely pathogenic

0.9856 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,200,842)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

ABCD1-related disorder

Computational evidence

Protein change
AlphaMissense	0.9856	likely pathogenic ✓ concordant with ClinVar
REVEL	0.947	strongly pathogenic-leaning
SaProt	LLR -14.82	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 12	GERP 1.7, phastCons 1
Regional constraint	o/e 0.38	unconstrained · MANE · 3,261 bp · p 4e-11 · regional, not allelic
Overall
CADD	27.9	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

No allele count reported in gnomAD v4.1 (AN 1,200,842). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ABCD1
Protein: p.Glu609Lys
Coding: c.1825G>A
dbSNP: rs150346282
Type: single nucleotide variant
Location: chrX:153743031 (GRCh38)

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

Disease context

ABCD1-related disorder

Also linked: adrenoleukodystrophy

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-glu609lys (accessed [today's date]).

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