PAX2 p.Arg71=
c.213G>A · VCV4909203
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00119%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.28 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 1.5, phastCons 1 |
| Overall | ||
| CADD | 21.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00119%
European (non-Finnish) · 14/1,179,964 alleles
Filtering AF
0.000688%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000539%
Overall
0.000867%
14/1,614,010 alleles · very rare
exomes 14/1,461,714 · genomes 0/152,296 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- PAX2
- Protein
- p.Arg71=
- Coding
- c.213G>A
- MANE Select
- NM_000278
- Type
- single nucleotide variant
- Location
- chr10:100750694 (GRCh38)
- Gene constraint
- LOEUF 0.451 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 61.52
- Residue 71
- a DNA-binding region; a UniProt-annotated variant site (in paprs); the 'pai subdomain' region
Similar variants
- PAX2 p.Arg71Gly Likely pathogenic ★ same residue
- PAX2 p.Arg71Met Likely pathogenic ★ same residue
- PAX2 p.Arg71Thr Pathogenic 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-arg71 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown