NFIX p.Val56del
c.166_168del · VCV4074588
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 2.8, phastCons 1 |
Variant & gene context
- Gene
- NFIX
- Protein
- p.Val56del
- Coding
- c.166_168del
- MANE Select
- NM_001365902
- Type
- Deletion
- Location
- chr19:13025158 (GRCh38)
- Gene constraint
- LOEUF 0.092 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.94 · 3 PDB
- Residue 56
- a DNA-binding region; an α-helix
Similar variants
- NFIX p.Val56Leu Uncertain significance ★ ⚠ same residue
- NFIX p.Arg486fs Pathogenic/Likely pathogenic ★★ same type
- NFIX p.Ile172fs Pathogenic ★★ same type
- NFIX c.697+3_697+6del Uncertain significance ★★ same type
- NFIX c.1104delG Pathogenic ★ same type
- NFIX p.Ala25fs Pathogenic ★ same type
- NFIX p.Ala355fs Pathogenic ★ same type
- NFIX p.Ala55fs 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/nfix-p-val56del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown