HPD c.596+7C>A
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 1,610,024)
Conditions
2
hawkinsinuria
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +7 | near-intronic (+7 nt from the splice site) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.1 | GERP -0.31, phastCons 1 |
| Non-coding constraint | Z 2.48 | 1 kb window · o/e 0.81 · regional · uncalibrated |
| Overall | ||
| CADD | 9.668 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,610,024). 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
- HPD
- Coding
- c.596+7C>A
- MANE Select
- NM_002150
- dbSNP
- rs1272021466
- Type
- single nucleotide variant
- Location
- chr12:121848992 (GRCh38)
- Gene constraint
- LOEUF 0.845 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.00 · 4 PDB
Disease context
hawkinsinuria — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: tyrosinemia type III
For Hawkinsinuria (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- Infancy, Neonatal
- Prevalence
- <1 / 1 000 000 (Worldwide)
Similar variants
- HPD p.Arg225Ter Pathogenic/Likely pathogenic ★★ same condition
- HPD p.Gln205Ter Pathogenic/Likely pathogenic ★★ same condition
- HPD p.Tyr160Cys Likely pathogenic ★★ ⚠ same condition
- HPD p.Ala230Thr Uncertain significance ★★ ⚠ same condition
- HPD p.Arg111Trp Uncertain significance ★★ ⚠ same condition
- HPD p.Arg119Gln Uncertain significance ★★ ⚠ same condition
- HPD p.Arg279Gly Uncertain significance ★★ ⚠ same condition
- HPD p.Arg300Trp Uncertain significance ★★ ⚠ 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/hpd-c-596-plus-7c-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown