NFKB1 p.Phe331=
c.993T>C · rs1578795505 · VCV739083
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.26 | acceptor loss, 7 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.5 | GERP -4.9 |
| Overall | ||
| CADD | 2.388 | PHRED · no single calibrated threshold — expert panels disagree |
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
- NFKB1
- Protein
- p.Phe331=
- Coding
- c.993T>C
- MANE Select
- NM_003998
- dbSNP
- rs1578795505
- Type
- single nucleotide variant
- Location
- chr4:102584747 (GRCh38)
- Gene constraint
- LOEUF 0.178 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 73.84 · 15 PDB
- Residue 331
- the rhd domain; a β-strand
Similar variants
- NFKB1 p.Phe331Cys Uncertain significance ★ ⚠ same residue
- NFKB1 p.Phe331fs Pathogenic ★ same residue
- NFKB1 c.159+1G>A Pathogenic/Likely pathogenic ★★ same type
- NFKB1 c.1753-1G>C Likely pathogenic ★★ same type
- NFKB1 c.407+1G>A Pathogenic/Likely pathogenic ★★ same type
- NFKB1 c.407+2T>G Pathogenic/Likely pathogenic ★★ same type
- NFKB1 c.835+2T>C Likely pathogenic ★★ same type
- NFKB1 c.928-1G>A 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/nfkb1-p-phe331 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown