GLB1 p.Asp159=
c.477C>T · VCV4961632
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,580,050)
Conditions
1
GLB1-related disorder
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 0.96 | GERP -2.9, phastCons 1 |
| Overall | ||
| CADD | 7.306 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,580,050). 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
- GLB1
- Protein
- p.Asp159=
- Coding
- c.477C>T
- MANE Select
- NM_000404
- Type
- single nucleotide variant
- Location
- chr3:33065538 (GRCh38)
- Gene constraint
- LOEUF 0.938 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 90.19 · 8 PDB
- Residue 159
- an α-helix
Similar variants
- GLB1 c.734-8A>G Likely pathogenic ★★ same condition
- GLB1 p.Ala301Val Pathogenic ★★ same condition
- GLB1 p.Arg201Cys Pathogenic/Likely pathogenic ★★ ⚠ same condition
- GLB1 p.Arg201His Pathogenic/Likely pathogenic ★★ ⚠ same condition
- GLB1 p.Arg208Cys Pathogenic ★★ ⚠ same condition
- GLB1 p.Arg457Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
- GLB1 p.Arg457Ter Pathogenic ★★ same condition
- GLB1 p.Arg590Cys 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/glb1-p-asp159 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown