PAX2 p.Arg243=
c.729G>A · VCV3905018
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.397 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.5 | GERP -4.2, phastCons 1 |
| Overall | ||
| CADD | 5.763 | 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
- PAX2
- Protein
- p.Arg243=
- Coding
- c.729G>A
- MANE Select
- NM_000278
- Type
- single nucleotide variant
- Location
- chr10:100806542 (GRCh38)
- Gene constraint
- LOEUF 0.451 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 61.52
Similar variants
- PAX2 p.Arg243Pro Uncertain significance ★★ ⚠ same residue
- PAX2 p.Arg243Gln Likely benign ★★ ⚠ same residue
- PAX2 p.Arg243Trp Uncertain significance ★ ⚠ same residue
- PAX2 c.212+1G>T Pathogenic/Likely pathogenic ★★ same type
- PAX2 c.213-8C>A Likely pathogenic ★★ same type
- PAX2 c.792+2T>C Pathogenic ★★ same type
- PAX2 p.Arg104Ter Pathogenic ★★ same type
- PAX2 p.Arg115Ter Pathogenic ★★ same type
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/pax2-p-arg243 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown