Is NFKB2 p.Pro884= (c.2652T>C) pathogenic?

NFKB2 p.Pro884= (c.2652T>C) is classified Likely benign in NFKB2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-21). No allele count reported in gnomAD v4.1 (AN 1,570,564); Associated with immunodeficiency, common variable, 10.

What condition is associated with NFKB2 p.Pro884= (c.2652T>C)?

NFKB2 p.Pro884= (c.2652T>C) is associated with immunodeficiency, common variable, 10 (ClinVar).

How common is NFKB2 p.Pro884= (c.2652T>C) in the general population?

NFKB2 p.Pro884= (c.2652T>C) is no allele count reported in gnomAD v4.1 (AN 1,570,564) (gnomAD).

NFKB2 p.Pro884=

c.2652T>C · rs2465742948 · VCV2005929

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,570,564)

Conditions

immunodeficiency, common variable, 10

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 -2.6	GERP -0.83
Overall
CADD	6.661	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,570,564). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: NFKB2
Protein: p.Pro884=
Coding: c.2652T>C
MANE Select: NM_001322934
dbSNP: rs2465742948
Type: single nucleotide variant
Location: chr10:102402325 (GRCh38)
Gene constraint: LOEUF 0.308 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 75.94 · 11 PDB
Residue 884: the 'disordered' region; a UniProt-annotated variant site (in truncated form eb308); a UniProt-annotated variant site (in truncated form p80ht); a UniProt-annotated variant site (in truncated form lb40)

Full NFKB2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

immunodeficiency, common variable, 10 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

NFKB2 p.Pro884Ala Uncertain significance ★★ ⚠ same residue
NFKB2 p.Arg853Ter Pathogenic ★★ same condition
NFKB2 p.Asp865Gly Pathogenic/Likely pathogenic ★★ same condition
NFKB2 p.Gln871Ter Pathogenic ★★ same condition
NFKB2 c.243+3G>A Uncertain significance ★★ same condition
NFKB2 p.Ala121Thr Uncertain significance ★★ ⚠ same condition
NFKB2 p.Ala363Thr Uncertain significance ★★ ⚠ same condition
NFKB2 p.Ala475Val Uncertain significance ★★ ⚠ 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/nfkb2-p-pro884 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown