AGXT c.423+36A>C
Uncertain significance
No assertion criteria
Classification
Uncertain significance
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
primary hyperoxaluria type 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +36 | near-intronic (+36 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.21 | GERP -0.83, phastCons 0.13 |
| Non-coding constraint | Z 3.64 | 1 kb window · o/e 0.78 · regional · uncalibrated |
| Overall | ||
| CADD | 4.919 | 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
- AGXT
- Coding
- c.423+36A>C
- MANE Select
- NM_000030
- dbSNP
- rs180177216
- Type
- single nucleotide variant
- Location
- chr2:240870744 (GRCh38)
- Gene constraint
- LOEUF 1.251 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 98.30 · 17 PDB
Disease context
primary hyperoxaluria type 1 — 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
- AGXT c.358+1G>A Pathogenic ★★ same condition
- AGXT c.359-2A>G Likely pathogenic ★★ same condition
- AGXT c.423+1G>A Pathogenic/Likely pathogenic ★★ same condition
- AGXT c.524+2T>A Likely pathogenic ★★ same condition
- AGXT c.525-1G>A Pathogenic ★★ same condition
- AGXT c.525-2A>T Pathogenic/Likely pathogenic ★★ same condition
- AGXT c.595+1G>T Pathogenic ★★ same condition
- AGXT c.596-2A>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/agxt-c-423-plus-36a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown