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Variant: NM_000033.4:c.649A>G

CA415099400

Gene: ABCD1 (HGNC:215)
Condition: adrenoleukodystrophy (MONDO:0018544)
Inheritance Mode: X-linked inheritance
UUID: 443be01c-2b2e-4d13-aac0-25e3b3726250
Approved on: 2026-04-16
Published on: 2026-04-16

HGVS expressions

NM_000033.4:c.649A>G
NC_000023.11:g.153725915A>G
CM000685.2:g.153725915A>G
NC_000023.10:g.152991370A>G
CM000685.1:g.152991370A>G
NC_000023.9:g.152644564A>G
NG_009022.2:g.6048A>G
NG_023231.1:g.3832T>C
ENST00000218104.6:c.649A>G
ENST00000218104.5:c.649A>G
ENST00000370129.4:c.94A>G
NM_000033.3:c.649A>G
More

Likely Pathogenic

Met criteria codes 6
PM2_Supporting PP4_Moderate PS3_Supporting PS4_Moderate PP1 PP3
Not Met criteria codes 1
PM5

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Peroxisomal Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for ABCD1 Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Peroxisomal Disorders VCEP
The variant c.649A>G (p.Lys217Glu) (NM_000033.4) is a missense variant in exon 1. At least one patient with this variant displayed Addison's disease/adrenal insufficiency, with positive family history (similarly affected sibling), and elevated VLCFAs. These symptoms are highly specific for adrenoleukodystrophy (PP4_Moderate, PMID: 11438993). This variant has been reported in at least 2 other probands meeting PP4_Supporting phenotype criteria (PS4_moderate; PMID: 11748843, 21300044). The ALD database (https://adrenoleukodystrophy.info/mutations-and-variants-in-abcd1) currently reports a total of 7 patients. The variant has been reported to segregate with adrenoleukodystrophy in ≥2 affected meioses from 1 family (PP1; PMID: 11438993). The computational predictor REVEL gives a score of 0.98, which is above the ClinGen Peroxisomal Disorders VCEP threshold of ≥0.85, evidence that correlates with impact to ABCD1 function (PP3). This variant is absent from gnomAD v4.1 (PM2_Supporting). Beta-oxidation assay in ALD patient fibroblasts transfected with the variant showed activity ≤26% of WT, indicating that this variant impacts protein function (PMID: 11438993)(PS3_Supporting). In summary, this variant meets the criteria to be classified as Likely Pathogenic for X-linked adrenoleukodystrophy based on the ACMG/AMP criteria applied, as specified by the ClinGen Peroxisomal VCEP: PP4_Moderate, PS4_moderate, PP1, PP3, PM2_supporting, PS3_supporting. (ClinGen Peroxisomal Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for ABCD1 Version 1.0.0)
Met criteria codes
PM2_Supporting
the variant is not present in gnomAD, v2.1, 3.1, 4.1
PP4_Moderate
At least one patient with this variant displayed Addison's disease/adrenal insufficiency (C), with positive family history (similarly affected sibling)(D), and elevated VLCFAs (F), which is highly specific for adrenoleukodystrophy (PP4_Moderate), PMID: 11438993).
PS3_Supporting
Dvorakova et al, (2001) performed in vitro mutagenesis of plasmid of the wt human cDNA to obtain variants identified in the in the two brothers. When transfected into X-ALD fibroblast (25% of WT beta-oxidation of VLCFA) K217E was not able to restore defective beta-oxidation, while the other variant (N13T) was able to restore to WT levels.
PS4_Moderate
There are at least 3 patients meeting PP4_supporting criteria counting towards PS4, in addition to the patient considered for PP4 and the two brothers included in PP1. The ALD db reports a total of 7 patients (likely include the fetus described in Lan F et al. 2011 and the unpublished in addition to 2 of PS4, 1 of PP4 and 2 of PP1)
PP1
Two brothers are described in Dvorakova et al., (2001) with isolated adrenal insufficiency (Addison disease, ADO). All patients in this study had elevated concentration of VLCFA in serum or plasma.
PP3
Revel score is confirmed to be 0.98, thus well above the specification threshold of 0.85 for pathogenicity.
Not Met criteria codes
PM5
c.649A>T p.Lys217* is listed as pathogenic, identified in a single ALD case (88).
Curation History
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