Is ABCD1 p.Pro49fs (c.146_159del) pathogenic?

ABCD1 p.Pro49fs (c.146159del) is classified Pathogenic in ABCD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-20). Absent from gnomAD; Associated with adrenoleukodystrophy.

What condition is associated with ABCD1 p.Pro49fs (c.146_159del)?

ABCD1 p.Pro49fs (c.146_159del) is associated with adrenoleukodystrophy (ClinVar).

How common is ABCD1 p.Pro49fs (c.146_159del) in the general population?

ABCD1 p.Pro49fs (c.146_159del) is absent from gnomAD (gnomAD).

How is X-linked adrenoleukodystrophy inherited?

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

ABCD1 p.Pro49fs

c.146_159del · rs1569540676 · VCV566603

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

adrenoleukodystrophy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 1 of 10
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.072	GERP -3.1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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.Pro49fs
Coding: c.146_159del
MANE Select: NM_000033
dbSNP: rs1569540676
Type: Deletion
Location: chrX:153725411 (GRCh38)
Structure: AlphaFold pLDDT 81.58 · 14 PDB

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.Pro49Ser Uncertain significance ★ ⚠ same residue
ABCD1 p.Pro49= Likely benign ★ same residue
ABCD1 c.1394-2_1404del Pathogenic/Likely pathogenic ★★ same condition
ABCD1 c.901-48_909del Pathogenic/Likely pathogenic ★★ same condition
ABCD1 p.Ala241fs Pathogenic ★★ same condition
ABCD1 p.Arg80_Leu82del Pathogenic/Likely pathogenic ★★ same condition
ABCD1 p.Gln472fs Pathogenic ★★ same condition
ABCD1 p.Gln645fs Pathogenic/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-pro49fs (accessed [today's date]).

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