AGA p.Leu7=
c.19T>C · rs2111028551 · VCV1117576
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
aspartylglucosaminuria
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.045 | GERP -3.3 |
| Overall | ||
| CADD | 3.378 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- AGA
- Protein
- p.Leu7=
- Coding
- c.19T>C
- MANE Select
- NM_000027
- dbSNP
- rs2111028551
- Type
- single nucleotide variant
- Location
- chr4:177442357 (GRCh38)
- Gene constraint
- LOEUF 0.938 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 91.41 · 2 PDB
Disease context
aspartylglucosaminuria — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Aspartylglucosaminuria (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Childhood
- Prevalence
- 1-9 / 1 000 000 (Australia)
Similar variants
- AGA p.Leu7Phe Uncertain significance ★ ⚠ same residue
- AGA c.127+1G>A Likely pathogenic ★★ same condition
- AGA c.127+1G>T Likely pathogenic ★★ same condition
- AGA c.128-2A>G Pathogenic ★★ same condition
- AGA c.281+1G>T Likely pathogenic ★★ same condition
- AGA c.395-8A>G Pathogenic/Likely pathogenic ★★ same condition
- AGA c.508-2A>C Likely pathogenic ★★ same condition
- AGA c.508-2A>G 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/aga-p-leu7 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown