NFKBIL1

NFKB inhibitor like 1

Basic information

Region (hg38): 6:31546870-31558829

Previous symbols: [ "NFKBIL" ]

Links

ENSG00000204498 ∙ NCBI:4795 ∙ OMIM:601022 ∙ HGNC:7800 ∙ Uniprot:Q9UBC1 ∙ 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 NFKBIL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NFKBIL1 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					1	1
missense			11	1	2	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	3

Variants in NFKBIL1

This is a list of pathogenic ClinVar variants found in the NFKBIL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31547563-T-A		Rheumatoid arthritis	risk factor (Feb 01, 2003)
6-31557636-G-A		not specified	Uncertain significance (Feb 16, 2023)
6-31557671-C-T		NFKBIL1-related disorder	Benign (Oct 17, 2019)
6-31557683-A-G		not specified	Uncertain significance (Aug 22, 2023)
6-31557745-C-T		not specified	Uncertain significance (Jan 03, 2024)
6-31557759-G-C		not specified	Uncertain significance (Dec 13, 2023)
6-31557780-C-G		not specified	Uncertain significance (Dec 16, 2023)
6-31558135-C-T		NFKBIL1-related disorder	Benign (Oct 17, 2019)
6-31558190-A-G		not specified	Uncertain significance (May 09, 2023)
6-31558196-G-A		not specified	Uncertain significance (Sep 27, 2022)
6-31558211-G-A		not specified	Uncertain significance (Feb 13, 2024)
6-31558217-G-A		NFKBIL1-related disorder	Benign (Jun 11, 2019)
6-31558279-C-G		NFKBIL1-related disorder	Likely benign (Apr 04, 2019)
6-31558301-C-G		not specified	Uncertain significance (Feb 23, 2023)
6-31558344-C-G		not specified	Uncertain significance (Jun 13, 2024)
6-31558352-G-T		not specified	Uncertain significance (Dec 07, 2021)
6-31558588-C-T		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NFKBIL1	protein_coding	protein_coding	ENST00000376148	4	11960

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0255	0.974	125663	0	20	125683	0.0000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.29	127	223	0.569	0.0000139	2383
Missense in Polyphen		41	89.692	0.45712		1015
Synonymous	2.27	57	83.3	0.684	0.00000429	799
Loss of Function	3.05	7	22.7	0.309	0.00000176	169

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000129	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000111	0.000106
Middle Eastern	0.00	0.00
South Asian	0.0000991	0.0000980
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the regulation of innate immune response. Acts as negative regulator of Toll-like receptor and interferon- regulatory factor (IRF) signaling pathways. Contributes to the negative regulation of transcriptional activation of NF-kappa-B target genes in response to endogenous proinflammatory stimuli. {ECO:0000269|PubMed:20829348}.

Intolerance Scores

• loftool: 0.950
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.118
• hipred: Y
• hipred_score: 0.572
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.918

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nfkbil1
• Phenotype: skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: I-kappaB kinase/NF-kappaB signaling;negative regulation of lipopolysaccharide-mediated signaling pathway;negative regulation of NF-kappaB transcription factor activity;negative regulation of tumor necrosis factor production;negative regulation of toll-like receptor signaling pathway;cytoplasmic sequestering of transcription factor;cellular response to lipopolysaccharide
• Cellular component: nucleus;cytosol
• Molecular function: protein binding