NFIX p.Val439fs
c.1315dup · VCV4686172
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 9 of 11 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 9.1 | GERP 0.19, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- NFIX
- Protein
- p.Val439fs
- Coding
- c.1315dup
- MANE Select
- NM_001365902
- Type
- Duplication
- Location
- chr19:13088048 (GRCh38)
- Gene constraint
- LOEUF 0.092 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 62.94 · 3 PDB
- Residue 439
- the 'disordered' region
Similar variants
- NFIX p.Arg363fs Pathogenic ★★ same type
- NFIX p.Glu17fs Pathogenic ★★ same type
- NFIX p.Gly160fs Pathogenic/Likely pathogenic ★★ same type
- NFIX p.Lys46delinsAlaTer Pathogenic/Likely pathogenic ★★ same type
- NFIX c.28-891dup Benign/Likely benign ★★ same type
- NFIX c.697+2dup Likely pathogenic ★ same type
- NFIX p.Ala364fs Pathogenic ★ same type
- NFIX p.Arg116fs 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-val439fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown