INF2 p.Lys15=
c.45G>A · VCV3750894
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000427%, 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 2.8 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 9.703 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000427%
European (non-Finnish) · 5/1,170,358 alleles
Filtering AF
0.000125%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9.1e-05%
Overall
0.000314%
5/1,594,642 alleles · very rare
exomes 4/1,442,386 · genomes 1/152,256 · 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.Lys15=
- Coding
- c.45G>A
- MANE Select
- NM_022489
- Type
- single nucleotide variant
- Location
- chr14:104701410 (GRCh38)
- Gene constraint
- LOEUF 0.526 · pLI 0.33 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 67.34 · 10 PDB
- Residue 15
- the gbd/fh3 domain; the 'disordered' region; an α-helix
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-lys15 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown