PAX2 p.Pro80=
c.240G>A · rs576772135 · VCV790302
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0538%, sas)
Conditions
2
renal coloboma syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -8.1 | GERP -5.2 |
| Overall | ||
| CADD | 0.988 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0538%
South Asian · 49/91,084 alleles
Filtering AF
0.0418%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0374%
Overall
0.00359%
58/1,614,206 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0538% | 1,859 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,837 |
| East Asian | 0.00223% | 44,878 |
| European (non-Finnish) | 0.000424% | 236,008 |
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.Pro80=
- Coding
- c.240G>A
- MANE Select
- NM_000278
- dbSNP
- rs576772135
- Type
- single nucleotide variant
- Location
- chr10:100750721 (GRCh38)
- Gene constraint
- LOEUF 0.451 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 61.52
- Residue 80
- a DNA-binding region; a UniProt-annotated variant site (in fsgs7; decreased dna-binding capability and transactivation ability)
Similar variants
- PAX2 p.Pro80Gln Likely pathogenic ★★ same residue
- PAX2 p.Pro80Leu Pathogenic/Likely pathogenic ★★ same residue
- PAX2 p.Pro80Ala 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
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-pro80 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown