The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000033.4(ABCD1):c.521A>G (p.Tyr174Cys)

CA415099025

458646 (ClinVar)

Gene: ABCD1 (HGNC:215)
Condition: adrenoleukodystrophy (MONDO:0018544)
Inheritance Mode: X-linked inheritance
UUID: 406a976d-39fc-4a01-9ee3-4217c8056e9a
Approved on: 2026-04-16
Published on: 2026-04-16

HGVS expressions

NM_000033.4:c.521A>G
NM_000033.4(ABCD1):c.521A>G (p.Tyr174Cys)
NC_000023.11:g.153725787A>G
CM000685.2:g.153725787A>G
NC_000023.10:g.152991242A>G
CM000685.1:g.152991242A>G
NC_000023.9:g.152644436A>G
NG_009022.2:g.5920A>G
NG_023231.1:g.3960T>C
ENST00000218104.6:c.521A>G
ENST00000218104.5:c.521A>G
NM_000033.3:c.521A>G
More

Pathogenic

Met criteria codes 7
PM2_Supporting PP4_Moderate PM6_Supporting PS3_Supporting PP1_Strong PS4 PP3
Not Met criteria codes 2
BS3 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 c.521A>G variant in ABCD1 is a missense variant predicted to cause substitution of tyrosine by cysteine at amino acid 174 (p.Tyr174Cys).At least one patient with this variant displayed rapid progression of inflammatory white matter demyelination in adolescence, had a X-linked pattern family history of disease including an affected male, and abnormal very long chain fatty acid testing, which is highly specific for adrenoleukodystrophy (PP4_Moderate, PMID:24722136). This variant has been reported in six more probands meeting a family history with an X-linked inheritance pattern where at least one family member is male or rapid progression of inflammatory white matter demyelination in childhood, and abnormal very long chain fatty acid testing (PS4; PMID:11336405, 28895702, 21068741, 26260157, 24722136). This variant has been assumed as a de novo occurrence with unconfirmed parental relationships in one individual with X-linked adrenoleukodystrophy (PM6_Supporting; PMID:11336405). The variant has been reported to segregate with X-linked adrenoleukodystrophy in eight affected family members from one family (PP1_Strong; PMID:11336405). This variant is absent from gnomAD v2.1.1, v3.1.2 and v4.1.0 (PM2_Supporting). Beta-oxidation assay in X-ALD fibroblasts (163T) showed that the beta-oxidation activity of the variant protein is approximately 5% of wild type ABCD1, indicating that this variant has an impact protein function (PMID:17542813)(PS3_Supporting). The computational predictor REVEL gives a score of 0.954, which is above the threshold of 0.85, evidence that correlates with impact to ABCD1 function (PP3). In summary, this variant meets the criteria to be classified as pathogenic for X-linked adrenoleukodystrophy based on ACMG/AMP criteria applied, as specified by the ClinGen Peroxisomal Disorders VCEP: PP1_Strong, PS4, PP3, PP4_Moderate, PM2_Supporting, PM6_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
This variant is absent from gnomAD v2.1.1, v3.1.2 and v4.1.0 (PM2_Supporting)
PP4_Moderate
At least one patient with this variant displayed rapid progression of inflammatory white matter demyelination in adolescence, had a X-linked pattern family history of disease including an affected male, and abnormal very long chain fatty acid testing, which is highly specific for adrenoleukodystrophy (PP4_Moderate, PMID:24722136).
PM6_Supporting
This variant has been assumed as a de novo occurrence with unconfirmed parental relationships in one individual with X-linked adrenoleukodystrophy (PM6_Supporting; PMID:11336405).
PS3_Supporting
Beta-oxidation assay in X-ALD fibroblasts (163T) showed that the beta-oxidation activity of the variant protein is approximately 5% of wild type ABCD1, indicating that this variant has an impact protein function (PMID:17542813)(PS3_Supporting).
PP1_Strong
The variant has been reported to segregate with X-linked adrenoleukodystrophy in eight affected family members from one family (PP1_Strong; PMID:11336405).
PS4
This variant has been reported in six more probands meeting a family history with an X-linked inheritance pattern where at least one family member is male or rapid progression of inflammatory white matter demyelination in childhood, and abnormal very long chain fatty acid testing (PS4; PMID:11336405, 28895702, 21068741, 26260157, 24722136).
PP3
The computational predictor REVEL gives a score of 0.954, which is above the threshold of 0.85, evidence that correlates with impact to ABCD1 function (PP3).
Not Met criteria codes
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
PM5 is not applied here, as pathogenic can be reached without it, so that it may be applied to these variants using this classification. (Tyr174His - LP, Tyr174Asp - P, Tyr174Ser - P/LP, Tyr174Ter- P)
Curation History
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