Is ABCD1 p.Val365fs (c.1093_1103del) pathogenic?

ABCD1 p.Val365fs (c.10931103del) is classified Likely pathogenic in ABCD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-10). Absent from gnomAD; Associated with congenital nervous system disorder.

What condition is associated with ABCD1 p.Val365fs (c.1093_1103del)?

ABCD1 p.Val365fs (c.1093_1103del) is associated with congenital nervous system disorder (ClinVar).

How common is ABCD1 p.Val365fs (c.1093_1103del) in the general population?

ABCD1 p.Val365fs (c.1093_1103del) is absent from gnomAD (gnomAD).

ABCD1 p.Val365fs

c.1093_1103del · rs2148395370 · VCV1180833

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

Conditions

congenital nervous system disorder

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 3 of 10
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.47	GERP -1.6, phastCons 0.056

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.Val365fs
Coding: c.1093_1103del
MANE Select: NM_000033
dbSNP: rs2148395370
Type: Deletion
Location: chrX:153736122 (GRCh38)
Structure: AlphaFold pLDDT 81.58 · 14 PDB
Residue 365: an α-helix; the abc transmembrane type-1 domain

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

Disease context

congenital nervous system disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ABCD1 p.Val365Met 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-val365fs (accessed [today's date]).

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