Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 14 submitters
gnomAD v4.1
Common
common (popmax 90.8%, eas) — too common for a highly-penetrant pathogenic allele
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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -6 | GERP -9.6 |
| Overall | ||
| CADD | 0.286 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
90.8%
East Asian · 39,775/43,800 alleles
Filtering AF
90.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 89.8%
Overall
56.4%
900,291/1,595,520 alleles · common
exomes 810,008/1,443,394 · genomes 90,283/152,126 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 90.8% | 1 |
| Admixed American | 68.4% | 1 |
| African / African-American | 64.3% | 2 |
| South Asian | 61.6% | 2 |
| Middle Eastern | 59.1% | 2 |
| Remaining individualsnot grpmax-eligible | 57.8% | 2 |
| Ashkenazi Jewishnot grpmax-eligible | 57.4% | 2 |
| European (non-Finnish) | 53.7% | 2 |
| Finnishnot grpmax-eligible | 53.1% | 2 |
| Amishnot grpmax-eligible | 53.1% | 2 |
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.Pro1069=
- Coding
- c.3207A>C
- MANE Select
- NM_022489
- dbSNP
- rs1128840
- Type
- single nucleotide variant
- Location
- chr14:104714369 (GRCh38)
- Gene constraint
- LOEUF 0.526 · pLI 0.33 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 67.34 · 10 PDB
- Residue 1069
- the 'disordered' region
Similar variants
- INF2 p.Pro1069Leu Likely benign ★★ same residue
- INF2 p.Pro1069Ser Uncertain significance ★ ⚠ same residue
- 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
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-pro1069 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown