Is ABCD1 p.Leu4fs (c.9_13del) pathogenic?

ABCD1 p.Leu4fs (c.913del) is classified Likely pathogenic in ABCD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-05). Absent from gnomAD.

How common is ABCD1 p.Leu4fs (c.9_13del) in the general population?

ABCD1 p.Leu4fs (c.9_13del) is absent from gnomAD (gnomAD).

ABCD1 p.Leu4fs

c.9_13del · rs2148388506 · VCV1322407

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 12	GERP 1.5, phastCons 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.Leu4fs
Coding: c.9_13del
MANE Select: NM_000033
dbSNP: rs2148388506
Type: Deletion
Location: chrX:153725274 (GRCh38)
Structure: AlphaFold pLDDT 81.58 · 14 PDB

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

Similar variants

ABCD1 p.Leu4= Likely benign ★ same residue
ABCD1 c.1394-2_1404del Pathogenic/Likely pathogenic ★★ same type
ABCD1 c.901-48_909del Pathogenic/Likely pathogenic ★★ same type
ABCD1 p.Ala241fs Pathogenic ★★ same type
ABCD1 p.Arg80_Leu82del Pathogenic/Likely pathogenic ★★ same type
ABCD1 p.Gln472fs Pathogenic ★★ same type
ABCD1 p.Gln645fs Pathogenic/Likely pathogenic ★★ same type
ABCD1 p.Glu371fs Pathogenic/Likely pathogenic ★★ same type

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-leu4fs (accessed [today's date]).

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