HGD p.Arg63=
c.189G>A · rs1390061303 · VCV2584767
Pathogenic
No assertion criteria
Classification
Pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
alkaptonuria
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 1.1 | GERP -0.13, phastCons 1 |
| Overall | ||
| CADD | 9.63 | 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
- HGD
- Protein
- p.Arg63=
- Coding
- c.189G>A
- MANE Select
- NM_000187
- dbSNP
- rs1390061303
- Type
- single nucleotide variant
- Location
- chr3:120670520 (GRCh38)
- Gene constraint
- LOEUF 1.199 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.85 · 2 PDB
- Residue 63
- a β-strand
Disease context
alkaptonuria — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Alkaptonuria (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adult, Infancy
- Prevalence
- 1-9 / 1 000 000 (Worldwide)
Similar variants
- HGD p.Arg63Ser Pathogenic/Likely pathogenic ★★ same residue
- HGD p.Arg63delinsIleTer Pathogenic same residue
- HGD c.1007-2A>T Pathogenic ★★ same condition
- HGD c.1188+1G>A Pathogenic ★★ same condition
- HGD c.15+1G>A Pathogenic/Likely pathogenic ★★ same condition
- HGD c.16-1G>A Pathogenic ★★ same condition
- HGD c.342+1G>A Pathogenic/Likely pathogenic ★★ same condition
- HGD c.342+1G>T 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/hgd-p-arg63 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown