NFRKB

protein-coding

nuclear factor related to kappaB binding protein, the group of INO80 complex

Gene summary

Enables protease binding activity. Involved in several processes, including positive regulation of DNA-templated transcription; regulation of DNA metabolic process; and regulation of chromosome organization. Located in Ino80 complex and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001143835.2

Inheritance

—

ClinVar variants

U:183B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chr11:129,863,636-129,895,590

External References & Databases

Ensembl (ENSG00000170322)

Transcript & Mutation Effects

hg38 • Region Span ~32.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NFRKB variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 180

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001143835.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			6 clinvar	3 clinvar		9
missense			174 clinvar	7 clinvar		181
nonsense						0
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	183	10	0	193

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 45 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001143835.2	RefSeq	NP_001137307.1	25	MANE Select
ENST00000682444.1	Ensembl	ENSP00000506850.1	25	MANE Select
NM_006165.4	RefSeq	NP_006156.2	25	Standard
ENST00000446488.7	Ensembl	ENSP00000400476.2	25	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Overview of nanoparticle effects
DNA Repair
Post-translational protein modification
Metabolism of proteins
UCH proteinases

Biological Process

DNA repair
DNA recombination
transcription by RNA polymerase II
inflammatory response
protein deubiquitination

Molecular Function

protease binding
DNA binding
protein binding

Cellular Component

nucleus
nucleoplasm
Ino80 complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000524794
Coding exons: 25
Length: 31955
Individuals with no LoFs: 125709
Homozygous LoFs: 0
Heterozygous LoFs: 39
Defined: 125748
p: 0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.53	659	779	0.845	0.0000473	8518
Missense (PolyPhen)		172	213.13	0.80701		2318
Synonymous	-1.66	343	306	1.12	0.0000187	2817
Loss of Function	5.58	15	62.7	0.239	0.00000330	697

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00018	rare
Latino/Admixed American	0.00021	0.00020	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00019	0.00017	rare
South Asian	0.00026	0.00026	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds to the DNA consensus sequence 5'-GGGGAATCTCC-3'. {ECO:0000269|PubMed:18922472}.;

Recessive Scores

pRec: 0.130

Intolerance Scores

LoFtool: 0.0267
RVIS EVS: -2.65
RVIS percentile EVS: 0.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): K
Indispensability pred.: E
Indispensability score: 0.632

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium