AGBL5 p.Leu753=
c.2259C>A · rs1669113453 · VCV3028774
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Conditions
1
inherited retinal dystrophy
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 0.65 | GERP -0.88, phastCons 0.29 |
| Overall | ||
| CADD | 6.77 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,876 alleles
Overall
6.84e-05%
1/1,461,790 alleles · very rare
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- AGBL5
- Protein
- p.Leu753=
- Coding
- c.2259C>A
- MANE Select
- NM_021831
- dbSNP
- rs1669113453
- Type
- single nucleotide variant
- Location
- chr2:27068648 (GRCh38)
- Gene constraint
- LOEUF 0.709 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.36 · 10 PDB
- Residue 753
- a UniProt-annotated variant site (found in patients with a usher-like phenotype encompassing rp and hearing loss; likely pathogenic); a UniProt-annotated variant site (in rp75)
Similar variants
- AGBL5 p.Trp592Ter Pathogenic ★★ same condition
- AGBL5 p.Arg147Cys Uncertain significance ★★ ⚠ same condition
- AGBL5 p.Arg341His Uncertain significance ★★ ⚠ same condition
- AGBL5 p.Arg487Gln Uncertain significance ★★ ⚠ same condition
- AGBL5 p.Arg489His Uncertain significance ★★ ⚠ same condition
- AGBL5 p.Arg537His Uncertain significance ★★ ⚠ same condition
- AGBL5 p.Arg598His Uncertain significance ★★ ⚠ same condition
- AGBL5 p.Arg673Trp Uncertain significance ★★ ⚠ 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/agbl5-p-leu753 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown