Is ASPA p.Glu293del (c.875AAG[1]) pathogenic?

ASPA p.Glu293del (c.875AAG[1]) is classified Uncertain significance in ASPA (ClinVar, No assertion criteria, 1 submitter; last evaluated 2017-02-17). Absent from gnomAD; Associated with Canavan disease.

What condition is associated with ASPA p.Glu293del (c.875AAG[1])?

ASPA p.Glu293del (c.875AAG[1]) is associated with Canavan disease (ClinVar).

How common is ASPA p.Glu293del (c.875AAG[1]) in the general population?

ASPA p.Glu293del (c.875AAG[1]) is absent from gnomAD (gnomAD).

How is Canavan disease inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

ASPA p.Glu293del

c.875AAG[1] · rs1555541321 · VCV550783

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Canavan disease

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.9	GERP 1.9, phastCons 1

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: ASPA
Protein: p.Glu293del
Coding: c.875AAG[1]
MANE Select: NM_000049
dbSNP: rs1555541321
Type: Microsatellite
Location: chr17:3499021 (GRCh38)
Gene constraint: LOEUF 1.098 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 96.14 · 8 PDB

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

Disease context

Canavan disease — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Canavan disease (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy, Neonatal

Similar variants

ASPA p.Glu293fs Pathogenic/Likely pathogenic ★★ same residue
ASPA p.Glu293= Likely benign ★ same residue
ASPA c.634+5_634+8del Pathogenic ★ same condition
ASPA p.Leu126fs Likely pathogenic ★ same condition
ASPA c.634+10_634+12del Likely benign ★ same condition
ASPA c.744+17_744+20del Likely benign ★ same condition
ASPA c.236+2T>C Likely pathogenic ★★ same condition
ASPA c.237-1G>T 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/aspa-p-glu293del (accessed [today's date]).

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