NFKBIZ

NFKB inhibitor zeta, the group of Ankyrin repeat domain containing

Basic information

Region (hg38): 3:101827990-101861022

Links

ENSG00000144802 ∙ NCBI:64332 ∙ OMIM:608004 ∙ HGNC:29805 ∙ Uniprot:Q9BYH8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hereditary nonpolyposis colon cancer (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NFKBIZ gene.

• Inborn genetic diseases (23 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NFKBIZ gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			22	2		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	2	0

Variants in NFKBIZ

This is a list of pathogenic ClinVar variants found in the NFKBIZ region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-101849668-G-C		not specified	Uncertain significance (Dec 27, 2022)
3-101849801-C-T		not specified	Uncertain significance (Jul 08, 2021)
3-101849803-G-A		not specified	Uncertain significance (Apr 05, 2023)
3-101849870-C-T		NFKBIZ-related disorder	Likely benign (Jun 05, 2020)
3-101849873-T-C		not specified	Uncertain significance (Sep 01, 2021)
3-101849911-C-A		NFKBIZ-related disorder	Likely benign (Jun 22, 2020)
3-101852171-C-T		not specified	Uncertain significance (Jan 27, 2022)
3-101852184-A-G		not specified	Uncertain significance (May 09, 2022)
3-101852897-A-G		not specified	Uncertain significance (Aug 09, 2021)
3-101852948-C-A		not specified	Uncertain significance (Dec 11, 2023)
3-101853115-G-A		not specified	Uncertain significance (Feb 13, 2024)
3-101853119-A-G		not specified	Uncertain significance (Oct 29, 2021)
3-101853253-G-A		not specified	Uncertain significance (Aug 04, 2021)
3-101853277-G-A		not specified	Uncertain significance (Feb 13, 2024)
3-101853323-C-T		not specified	Uncertain significance (Aug 22, 2023)
3-101853350-G-C			Uncertain significance (Aug 12, 2019)
3-101853377-C-T		not specified	Uncertain significance (Dec 28, 2022)
3-101853386-A-G		not specified	Uncertain significance (May 31, 2023)
3-101853466-C-T		not specified	Likely benign (Sep 12, 2023)
3-101853467-C-G		not specified	Uncertain significance (Jun 30, 2023)
3-101853473-C-G		not specified	Uncertain significance (Jan 05, 2022)
3-101853528-T-G		not specified	Uncertain significance (Nov 03, 2023)
3-101853548-T-C		not specified	Likely benign (Aug 17, 2022)
3-101853587-C-G		not specified	Uncertain significance (Jan 27, 2022)
3-101853700-T-G		not specified	Uncertain significance (Sep 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NFKBIZ	protein_coding	protein_coding	ENST00000326172	12	33032

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000193	125746	0	2	125748	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.18	299	362	0.825	0.0000188	4695
Missense in Polyphen		60	105.5	0.56872		1355
Synonymous	-1.23	156	138	1.13	0.00000749	1405
Loss of Function	5.02	2	33.2	0.0602	0.00000169	372

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in regulation of NF-kappa-B transcription factor complexes. Inhibits NF-kappa-B activity without affecting its nuclear translocation upon stimulation. Inhibits DNA-binding of RELA and NFKB1/p50, and of the NF-kappa-B p65-p50 heterodimer and the NF-kappa-B p50-p50 homodimer. Seems also to activate NF- kappa-B-mediated transcription. In vitro, upon association with NFKB1/p50 has transcriptional activation activity and, together with NFKB1/p50 and RELA, is recruited to LCN2 promoters. Promotes transcription of LCN2 and DEFB4. Is recruited to IL-6 promoters and activates IL-6 but decreases TNF-alpha production in response to LPS. Seems to be involved in the induction of inflammatory genes activated through TLR/IL-1 receptor signaling. May promote apoptosis (By similarity). Involved in the induction of T helper 17 cells (Th17) differentiation upon recognition of antigen by T cell antigen receptor (TCR) (By similarity). {ECO:0000250, ECO:0000250|UniProtKB:Q9EST8, ECO:0000269|PubMed:16513645, ECO:0000269|PubMed:16622025}.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human);TNFalpha (Consensus)

Recessive Scores

• pRec: 0.0971

Intolerance Scores

• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.31

Haploinsufficiency Scores

• pHI: 0.491
• hipred: Y
• hipred_score: 0.739
• ghis: 0.493

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.373

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nfkbiz
• Phenotype: immune system phenotype; vision/eye phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: inflammatory response;positive regulation of inflammatory response;T cell receptor signaling pathway;positive regulation of T-helper 17 cell differentiation
• Cellular component: nucleus;nuclear speck;cytoplasmic ribonucleoprotein granule
• Molecular function: protein binding