HGD p.Pro66=
c.198T>C · rs2107548808 · VCV1611495
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,604,248)
Conditions
1
alkaptonuria
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 1.1 | GERP -2, phastCons 0.99 |
| Overall | ||
| CADD | 8.663 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,604,248). 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
- HGD
- Protein
- p.Pro66=
- Coding
- c.198T>C
- MANE Select
- NM_000187
- dbSNP
- rs2107548808
- Type
- single nucleotide variant
- Location
- chr3:120670511 (GRCh38)
- Gene constraint
- LOEUF 1.199 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.85 · 2 PDB
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 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
- HGD c.342+3A>C Pathogenic/Likely pathogenic ★★ same condition
- HGD c.469+1G>C 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-pro66 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown