NFKB1 p.Lys897=
c.2691G>A · rs372519363 · VCV1550402
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0187%, afr)
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 | GERP 0.28, phastCons 0.99 |
| Overall | ||
| CADD | 7.457 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0187%
African / African-American · 14/74,852 alleles
Filtering AF
0.0112%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00905%
Overall
0.00112%
18/1,613,748 alleles · ultra-rare
exomes 11/1,461,692 · genomes 7/152,056 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0187% | 5,347 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,821 |
| Admixed American | 0.00167% | 59,992 |
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
- NFKB1
- Protein
- p.Lys897=
- Coding
- c.2691G>A
- MANE Select
- NM_003998
- dbSNP
- rs372519363
- Type
- single nucleotide variant
- Location
- chr4:102613523 (GRCh38)
- Gene constraint
- LOEUF 0.178 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 73.84 · 15 PDB
- Residue 897
- the 'interaction with cflar' region
Similar variants
- 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
- NFKB1 p.Arg157Ter Pathogenic ★★ same type
- NFKB1 p.Arg284Ter 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/nfkb1-p-lys897 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown