PAX2 p.Val65=
c.195C>G · rs1845371308 · VCV3031569
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
Conditions
2
renal coloboma syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.27 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 6 | GERP 2.6, phastCons 1 |
| Overall | ||
| CADD | 16.86 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,892 alleles
Overall
6.2e-05%
1/1,612,484 alleles · very rare
exomes 1/1,460,110 · genomes 0/152,374 · 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.Val65=
- Coding
- c.195C>G
- MANE Select
- NM_000278
- dbSNP
- rs1845371308
- Type
- single nucleotide variant
- Location
- chr10:100749897 (GRCh38)
- Gene constraint
- LOEUF 0.451 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 61.52
- Residue 65
- a DNA-binding region; a UniProt-annotated variant site (in paprs); the 'pai subdomain' region
Similar variants
- PAX2 p.Val65Ala Uncertain significance ★ ⚠ same residue
- PAX2 c.212+1G>T Pathogenic/Likely pathogenic ★★ same condition
- PAX2 c.213-8C>A Likely pathogenic ★★ same condition
- PAX2 c.792+2T>C Pathogenic ★★ same condition
- PAX2 p.Arg104Ter Pathogenic ★★ same condition
- PAX2 p.Arg115Ter Pathogenic ★★ same condition
- PAX2 p.Arg140Trp Pathogenic ★★ same condition
- PAX2 p.Arg229Ter 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/pax2-p-val65 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown