NFIB p.Ser379=
c.1137G>A · rs746059013 · VCV2673168
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00892%, eas)
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 -3.9 | GERP -5.3 |
| Overall | ||
| CADD | 8.34 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00892%
East Asian · 4/44,862 alleles
Filtering AF
0.00298%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0018%
Overall
0.000496%
8/1,613,796 alleles · very rare
exomes 8/1,461,720 · genomes 0/152,076 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00892% | 11,216 |
| European (non-Finnish) | 0.000339% | 294,982 |
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
- NFIB
- Protein
- p.Ser379=
- Coding
- c.1137G>A
- MANE Select
- NM_001190737
- dbSNP
- rs746059013
- Type
- single nucleotide variant
- Location
- chr9:14120548 (GRCh38)
- Gene constraint
- LOEUF 0.3 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 68.17 · 2 PDB
- Residue 379
- a UniProt-annotated variant site (in macid); the 'disordered' region
Similar variants
- NFIB p.Ser379Trp Uncertain significance ★ ⚠ same residue
- NFIB p.Arg301Ter Pathogenic/Likely pathogenic ★★ same type
- NFIB p.Arg37Ter Pathogenic ★★ same type
- NFIB p.Arg39Cys Pathogenic/Likely pathogenic ★★ same type
- NFIB p.Arg48Ter Pathogenic/Likely pathogenic ★★ same type
- NFIB p.Arg89Ter Pathogenic/Likely pathogenic ★★ same type
- NFIB p.Gln123Ter Likely pathogenic ★★ same type
- NFIB p.Leu132Pro Pathogenic/Likely 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/nfib-p-ser379 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown