NFKBID

NFKB inhibitor delta, the group of Ankyrin repeat domain containing

Basic information

Region (hg38): 19:35887630-35902303

Links

ENSG00000167604 ∙ NCBI:84807 ∙ OMIM:618887 ∙ HGNC:15671 ∙ Uniprot:Q8NI38 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NFKBID 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			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	0

Variants in NFKBID

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

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

Position	Type	Phenotype	Significance	ClinVar
19-35888587-C-T		not specified	Uncertain significance (Apr 09, 2024)
19-35888588-G-A		not specified	Uncertain significance (Jan 20, 2025)
19-35888609-G-A		not specified	Uncertain significance (Jan 27, 2025)
19-35889892-C-G		not specified	Uncertain significance (Feb 07, 2025)
19-35889912-C-G		not specified	Uncertain significance (May 12, 2024)
19-35889922-G-T		not specified	Uncertain significance (May 03, 2023)
19-35889925-C-T		not specified	Uncertain significance (Jul 02, 2024)
19-35889985-G-A		not specified	Uncertain significance (Dec 11, 2024)
19-35889999-T-G		not specified	Uncertain significance (Mar 21, 2023)
19-35890005-G-A		Immunodeficiency, common variable, 12	Uncertain significance (May 21, 2020)
19-35890006-G-C		not specified	Uncertain significance (Mar 07, 2024)
19-35890405-C-T		not specified	Uncertain significance (Jan 31, 2024)
19-35890406-G-A		not specified	Uncertain significance (Nov 15, 2021)
19-35896049-G-T		not specified	Uncertain significance (Aug 26, 2024)
19-35896080-C-A		Immunodeficiency, common variable, 12	Uncertain significance (May 21, 2020)
19-35896080-C-T		not specified	Likely benign (Apr 27, 2024)
19-35896421-C-T		not specified	Uncertain significance (Mar 06, 2025)
19-35896459-G-A		not specified	Uncertain significance (Jun 07, 2024)
19-35896462-T-C		not specified	Uncertain significance (Sep 01, 2021)
19-35896754-C-T		not specified	Likely benign (Jun 11, 2021)
19-35896757-C-T		not specified	Uncertain significance (Jun 16, 2023)
19-35896779-C-A		not specified	Uncertain significance (Feb 14, 2024)
19-35896781-G-A		not specified	Uncertain significance (Nov 09, 2024)
19-35896791-C-A		not specified	Uncertain significance (Nov 26, 2024)
19-35896799-C-T		not specified	Uncertain significance (Jul 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NFKBID	protein_coding	protein_coding	ENST00000396901	9	14651

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.319	0.680	124641	0	6	124647	0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.03	124	206	0.602	0.0000132	1957
Missense in Polyphen		38	92.223	0.41205		973
Synonymous	0.217	89	91.6	0.971	0.00000611	714
Loss of Function	2.94	4	17.2	0.233	0.00000100	165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000165	0.000165
Ashkenazi Jewish	0.000103	0.0000997
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000181	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates the expression of IL-2, IL-6, and other cytokines through regulation on NF-kappa-B activity. Functions in the regulation of inflammatory responses. Involved in the induction of T helper 17 cells (Th17) differentiation upon recognition of antigen by T cell antigen receptor (TCR). May also regulate TCR-induced negative selection of thymocytes. {ECO:0000250|UniProtKB:Q2TB02}.

Recessive Scores

• pRec: 0.0946

Intolerance Scores

• loftool: 0.317
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.58

Haploinsufficiency Scores

• pHI: 0.142
• hipred: Y
• hipred_score: 0.523
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.421

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nfkbid
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; hematopoietic system phenotype; digestive/alimentary phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: inflammatory response;negative regulation of NF-kappaB transcription factor activity;negative regulation of T cell differentiation in thymus;negative regulation of I-kappaB kinase/NF-kappaB signaling;T cell receptor signaling pathway;positive regulation of thymocyte apoptotic process;positive regulation of T-helper 17 cell differentiation
• Cellular component: nucleus
• Molecular function: protein binding;NF-kappaB binding