PAX2 p.Phe245=
c.735T>C · rs746316295 · VCV1571359
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00492%, nfe)
Conditions
2
renal coloboma syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.376 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP -0.036, phastCons 1 |
| Overall | ||
| CADD | 8.943 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00492%
European (non-Finnish) · 58/1,180,046 alleles
Filtering AF
0.00386%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00353%
Overall
0.00372%
60/1,614,098 alleles · very rare
exomes 58/1,461,864 · genomes 2/152,234 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00492% | 20,346 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,243 |
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.Phe245=
- Coding
- c.735T>C
- MANE Select
- NM_000278
- dbSNP
- rs746316295
- Type
- single nucleotide variant
- Location
- chr10:100806548 (GRCh38)
- Gene constraint
- LOEUF 0.451 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 61.52
Similar variants
- 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
- PAX2 p.Gly24Val Likely 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-phe245 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown