Is PAX2 p.Pro32= (c.96C>G) pathogenic?

PAX2 p.Pro32= (c.96C>G) is classified Likely benign in PAX2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-03-31). Ultra-rare (popmax 0.0627%, sas); Associated with renal coloboma syndrome.

What condition is associated with PAX2 p.Pro32= (c.96C>G)?

PAX2 p.Pro32= (c.96C>G) is associated with renal coloboma syndrome, focal segmental glomerulosclerosis 7 (ClinVar).

How common is PAX2 p.Pro32= (c.96C>G) in the general population?

PAX2 p.Pro32= (c.96C>G) is ultra-rare (popmax 0.0627%, sas) (gnomAD).

PAX2 p.Pro32=

c.96C>G · rs757633295 · VCV1609814

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0627%, sas)

Conditions

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 4	GERP 1.5, phastCons 1
Overall
CADD	15.13	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0627% South Asian · 57/90,878 alleles

Filtering AF 0.0497% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.045%

Overall 0.00676% 109/1,612,068 alleles · ultra-rare exomes 101/1,459,726 · genomes 8/152,342 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0627%	1,594
East Asian	0.0513%	1,949
Remaining individualsnot grpmax-eligible	0.0144%	6,937
European (non-Finnish)	0.00161%	62,049
Finnishnot grpmax-eligible	0.00157%	63,512

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.Pro32=
Coding: c.96C>G
MANE Select: NM_000278
dbSNP: rs757633295
Type: single nucleotide variant
Location: chr10:100749798 (GRCh38)
Gene constraint: LOEUF 0.451 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 61.52
Residue 32: a DNA-binding region; the 'pai subdomain' region

Full PAX2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

renal coloboma syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: focal segmental glomerulosclerosis 7

Similar variants

PAX2 p.Pro32Thr Likely pathogenic ★ same residue
PAX2 p.Pro32Leu 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

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-pro32 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown