PAX2 p.Phe10=
c.30C>T · VCV4849188
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00439%, sas)
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 7.5 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 16.58 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00439%
South Asian · 4/91,018 alleles
Filtering AF
0.00143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000435%
7/1,609,870 alleles · very rare
exomes 5/1,457,808 · genomes 2/152,062 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00439% | 22,754 |
| African / African-American | 0.00401% | 24,931 |
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.Phe10=
- Coding
- c.30C>T
- MANE Select
- NM_000278
- Type
- single nucleotide variant
- Location
- chr10:100746290 (GRCh38)
- Gene constraint
- LOEUF 0.451 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 61.52
Similar variants
- PAX2 p.Phe10fs Likely pathogenic ★ same residue
- PAX2 c.212+1G>T Pathogenic/Likely pathogenic ★★ same type
- PAX2 c.213-8C>A Likely pathogenic ★★ same type
- PAX2 c.792+2T>C Pathogenic ★★ same type
- PAX2 p.Arg104Ter Pathogenic ★★ same type
- PAX2 p.Arg115Ter Pathogenic ★★ same type
- PAX2 p.Arg140Trp Pathogenic ★★ same type
- PAX2 p.Arg229Ter Pathogenic ★★ same type
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-phe10 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown