NFIB p.Arg89Ter
c.265C>T · rs764333096 · VCV424344
Pathogenic/Likely pathogenic
Multiple submitters
Classification
Pathogenic/Likely pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 10 submitters
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
2
intellectual disability
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 2 of 11 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.5, phastCons 1 |
| Overall | ||
| CADD | 57.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- NFIB
- Protein
- p.Arg89Ter
- Coding
- c.265C>T
- MANE Select
- NM_001190737
- dbSNP
- rs764333096
- Type
- single nucleotide variant
- Location
- chr9:14307286 (GRCh38)
- Gene constraint
- LOEUF 0.3 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 68.17 · 2 PDB
- Residue 89
- a DNA-binding region; a UniProt-annotated variant site (in macid)
Similar variants
- NFIB p.Arg301Ter Pathogenic/Likely pathogenic ★★ same condition
- NFIB p.Arg37Ter Pathogenic ★★ same condition
- NFIB p.Arg39Cys Pathogenic/Likely pathogenic ★★ same condition
- NFIB p.Arg48Ter Pathogenic/Likely pathogenic ★★ same condition
- NFIB p.Gln123Ter Likely pathogenic ★★ same condition
- NFIB p.Leu132Pro Pathogenic/Likely pathogenic ★★ same condition
- NFIB p.Lys126Glu Pathogenic/Likely pathogenic ★★ same condition
- NFIB p.Ser356Ter 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/nfib-p-arg89ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown