Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 12 submitters
gnomAD v4.1
Common
common (popmax 75.1%, afr) — too common for a highly-penetrant pathogenic allele
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 -5.2 | GERP -3.5 |
| Overall | ||
| CADD | 0.634 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
75.1%
African / African-American · 56,276/74,934 alleles
Filtering AF
74.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 74.4%
Overall
29.7%
479,157/1,612,774 alleles · common
exomes 419,175/1,460,664 · genomes 59,982/152,110 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 75.1% | 1 |
| Middle Eastern | 41% | 2 |
| South Asian | 32.3% | 3 |
| Amishnot grpmax-eligible | 32.1% | 3 |
| Remaining individualsnot grpmax-eligible | 30.9% | 3 |
| European (non-Finnish) | 28.4% | 4 |
| Ashkenazi Jewishnot grpmax-eligible | 25.2% | 4 |
| Admixed American | 21.9% | 5 |
| Finnishnot grpmax-eligible | 18.3% | 5 |
| East Asian | 9.97% | 10 |
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.Pro303=
- Coding
- c.909A>C
- MANE Select
- NM_000278
- dbSNP
- rs1800898
- Type
- single nucleotide variant
- Location
- chr10:100809226 (GRCh38)
- Gene constraint
- LOEUF 0.451 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 61.52
Similar variants
- PAX2 p.Pro303Ala 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-pro303 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown