INF2 p.Pro501=
c.1503C>T · rs1057520913 · VCV380889
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00602%, nfe)
Conditions
2
focal segmental glomerulosclerosis 5
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.1 | GERP -2.7 |
| Overall | ||
| CADD | 0.668 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00602%
European (non-Finnish) · 59/980,352 alleles
Filtering AF
0.00474%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00434%
Overall
0.00435%
59/1,355,404 alleles · very rare
exomes 57/1,205,844 · genomes 2/149,560 · joint denominator
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
- INF2
- Protein
- p.Pro501=
- Coding
- c.1503C>T
- MANE Select
- NM_022489
- dbSNP
- rs1057520913
- Type
- single nucleotide variant
- Location
- chr14:104707770 (GRCh38)
- Gene constraint
- LOEUF 0.526 · pLI 0.33 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 67.34 · 10 PDB
Similar variants
- INF2 p.Arg177Cys Pathogenic/Likely pathogenic ★★ same condition
- INF2 p.Arg214Cys Pathogenic/Likely pathogenic ★★ same condition
- INF2 p.Arg214His Pathogenic/Likely pathogenic ★★ same condition
- INF2 p.Arg218Gln Pathogenic/Likely pathogenic ★★ same condition
- INF2 p.Arg218Trp Pathogenic/Likely pathogenic ★★ same condition
- INF2 p.Arg91Gly Pathogenic/Likely pathogenic ★★ same condition
- INF2 p.Asn202Asp Likely pathogenic ★★ same condition
- INF2 p.Glu184Lys 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/inf2-p-pro501 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown