GRHPR p.Glu18=
c.54G>A · VCV4293436
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
primary hyperoxaluria type 2
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.73 | donor loss · deltas |
|---|---|---|
| Pangolin | Δ0.50 | loss · gain 0.37 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 2.6 | GERP -1, phastCons 1 |
| Overall | ||
| CADD | 2.317 | 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
- GRHPR
- Protein
- p.Glu18=
- Coding
- c.54G>A
- MANE Select
- NM_012203
- Type
- single nucleotide variant
- Location
- chr9:37422804 (GRCh38)
- Gene constraint
- LOEUF 1.313 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 96.80 · 4 PDB
- Residue 18
- an α-helix
Disease context
primary hyperoxaluria type 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Primary hyperoxaluria (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- All ages
- Prevalence
- 1-9 / 1 000 000 (Germany)
Similar variants
- GRHPR p.Glu18Lys Uncertain significance ★ ⚠ same residue
- GRHPR c.404+5G>A Likely pathogenic ★★ same condition
- GRHPR c.493+2T>A Pathogenic/Likely pathogenic ★★ same condition
- GRHPR c.494-2A>G Pathogenic/Likely pathogenic ★★ same condition
- GRHPR c.734+1G>A Pathogenic/Likely pathogenic ★★ same condition
- GRHPR c.735-1G>A Pathogenic/Likely pathogenic ★★ same condition
- GRHPR c.83+1G>C Pathogenic/Likely pathogenic ★★ same condition
- GRHPR c.84-2A>G 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/grhpr-p-glu18 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown