GLB1 p.Phe107=
c.321T>C · rs2471437886 · VCV2944092
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
2
mucopolysaccharidosis type 4B
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.054 | GERP -4.2, phastCons 0.001 |
| Overall | ||
| CADD | 5.023 | 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
- GLB1
- Protein
- p.Phe107=
- Coding
- c.321T>C
- MANE Select
- NM_000404
- dbSNP
- rs2471437886
- Type
- single nucleotide variant
- Location
- chr3:33068895 (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 107
- an α-helix
Disease context
mucopolysaccharidosis type 4B — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: GM1 gangliosidosis
For Mucopolysaccharidosis type 4 (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Childhood, Infancy
- Prevalence
- <1 / 1 000 000 (Sweden)
Similar variants
- GLB1 p.Phe107Leu Likely pathogenic ★★ same residue
- GLB1 c.1144-2A>G Pathogenic/Likely pathogenic ★★ same condition
- GLB1 c.1233+1G>A Pathogenic/Likely pathogenic ★★ same condition
- GLB1 c.1347+1G>T Likely pathogenic ★★ same condition
- GLB1 c.1479+1G>A Pathogenic ★★ same condition
- GLB1 c.1480-2A>G Pathogenic ★★ same condition
- GLB1 c.245+1G>A Pathogenic ★★ same condition
- GLB1 c.396+2T>C Pathogenic/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/glb1-p-phe107 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown