IL12RB1

interleukin 12 receptor subunit beta 1, the group of Fibronectin type III domain containing|CD molecules|Interleukin receptors

Basic information

Region (hg38): 19:18058995-18098944

Previous symbols: [ "IL12RB" ]

Links

ENSG00000096996 ∙ NCBI:3594 ∙ OMIM:601604 ∙ HGNC:5971 ∙ Uniprot:P42701 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency (Strong), mode of inheritance: AR
• Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Immunodeficiency 30	AR	Allergy/Immunology/Infectious	Individuals have been described as susceptible to severe atypical mycobacterial infections (as well as other infections, including Salmonella, Cryptococcal, Coccidioides infections), and prophylaxis and early and aggressive treatment of infections may be beneficial; Consideration of potential adverse effects of BCG vaccination in some individuals may be beneficial	Allergy/Immunology/Infectious	9603732; 9603733; 12591909; 15736007; 21905505; 21258095; 22523911; 23864330

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IL12RB1 gene.

• Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency (35 variants)
• not provided (4 variants)
• Mycobacterium tuberculosis, susceptibility to (1 variants)
• Inherited Immunodeficiency Diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL12RB1 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			5	91	6	102
missense	3	1	188	16	7	215
nonsense	16	1				17
start loss						0
frameshift	11	1	1			13
inframe indel			1			1
splice donor/acceptor (+/-2bp)	5	5	2			12
splice region			18	14	1	33
non coding		2	6	46	16	70
Total	35	10	203	153	29

Highest pathogenic variant AF is 0.0000987

Variants in IL12RB1

This is a list of pathogenic ClinVar variants found in the IL12RB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-18059574-G-A		Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency • not specified	Benign (Jan 24, 2024)
19-18059578-G-A		Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency	Uncertain significance (Jan 12, 2018)
19-18059608-T-C		Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency	Uncertain significance (Jun 08, 2023)
19-18059614-C-T		Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency	Uncertain significance (Jun 29, 2019)
19-18059622-T-TACAACA		Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency	Likely benign (Jan 19, 2021)
19-18059625-A-G		Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency	Likely benign (Aug 16, 2021)
19-18059847-C-A		not specified	Benign (Jan 24, 2024)
19-18059870-G-A		not specified	Benign (Jan 24, 2024)
19-18059877-C-T		Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency	Uncertain significance (Jul 17, 2022)
19-18059878-C-T		Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency	Likely benign (Nov 22, 2021)
19-18059879-A-G		Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency	Likely benign (Nov 20, 2023)
19-18059884-G-A		Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency	Likely benign (Mar 13, 2023)
19-18059890-G-A		Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency	Uncertain significance (Mar 26, 2022)
19-18059901-T-C		Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency	Uncertain significance (Aug 17, 2023)
19-18059905-A-G		Inborn genetic diseases • Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency	Uncertain significance (May 11, 2022)
19-18059917-C-T		Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency	Likely benign (Jan 05, 2024)
19-18059963-A-G		Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency • IL12RB1-related disorder	Conflicting classifications of pathogenicity (Jan 15, 2024)
19-18059965-G-A		Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency • Inborn genetic diseases	Uncertain significance (Apr 22, 2024)
19-18059975-C-T		Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency	Likely benign (Aug 14, 2019)
19-18059980-C-A		Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency	Pathogenic (Jun 04, 2023)
19-18059981-G-A		Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency	Likely benign (Jun 13, 2022)
19-18059981-G-C		Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency	Likely benign (Aug 26, 2022)
19-18059998-C-T		Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency • IL12RB1-related disorder	Likely benign (Dec 30, 2023)
19-18059999-G-A		Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency	Uncertain significance (Jul 12, 2022)
19-18060000-C-T		Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency	Uncertain significance (Oct 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL12RB1	protein_coding	protein_coding	ENST00000600835	17	39950

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.36e-15	0.861	125614	0	134	125748	0.000533

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.237	377	390	0.966	0.0000240	4231
Missense in Polyphen		80	89.989	0.889		1028
Synonymous	-0.535	182	173	1.05	0.0000117	1336
Loss of Function	2.03	29	43.5	0.667	0.00000240	425

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000791	0.000764
Ashkenazi Jewish	0.000496	0.000496
East Asian	0.000331	0.000326
Finnish	0.000190	0.000185
European (Non-Finnish)	0.000764	0.000747
Middle Eastern	0.000331	0.000326
South Asian	0.000466	0.000457
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as an interleukin receptor which binds interleukin-12 with low affinity and is involved in IL12 transduction. Associated with IL12RB2 it forms a functional, high affinity receptor for IL12. Associates also with IL23R to form the interleukin-23 receptor which functions in IL23 signal transduction probably through activation of the Jak-Stat signaling cascade. {ECO:0000269|PubMed:12023369}.
• Disease: DISEASE: Immunodeficiency 30 (IMD30) [MIM:614891]: A form of Mendelian susceptibility to mycobacterial disease, a rare condition caused by impairment of interferon-gamma mediated immunity. It is characterized by predisposition to illness caused by moderately virulent mycobacterial species, such as Bacillus Calmette-Guerin (BCG) vaccine, environmental non-tuberculous mycobacteria, and by the more virulent Mycobacterium tuberculosis. Other microorganisms rarely cause severe clinical disease in individuals with susceptibility to mycobacterial infections, with the exception of Salmonella which infects less than 50% of these individuals. Clinical outcome severity depends on the degree of impairment of interferon-gamma mediated immunity. Some patients die of overwhelming mycobacterial disease with lepromatous-like lesions in early childhood, whereas others develop, later in life, disseminated but curable infections with tuberculoid granulomas. IMD30 has low penetrance, and affected individuals have relatively mild disease and good prognosis. BCG disease and salmonellosis are the most frequent infections in IMD30 patients. {ECO:0000269|PubMed:11424023}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Jak-STAT signaling pathway - Homo sapiens (human);Inflammatory bowel disease (IBD) - Homo sapiens (human);Th17 cell differentiation - Homo sapiens (human);Th1 and Th2 cell differentiation - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);JAK-STAT-Core;no2-dependent il-12 pathway in nk cells;Interleukin-12 family signaling;Signaling by Interleukins;il12 and stat4 dependent signaling pathway in th1 development;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;IL-12 signaling;Immune System;IL-23 signaling;Interleukin-23 signaling;JAK STAT MolecularVariation 2;JAK STAT pathway and regulation;Interleukin-12 signaling;IL23-mediated signaling events;IL27-mediated signaling events;IL12-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.329

Intolerance Scores

• loftool: 0.415
• rvis_EVS: 0.41
• rvis_percentile_EVS: 76.54

Haploinsufficiency Scores

• pHI: 0.0953
• hipred: N
• hipred_score: 0.366
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.827

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Il12rb1
• Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype

Gene ontology

• Biological process: positive regulation of T cell mediated cytotoxicity;positive regulation of defense response to virus by host;positive regulation of T-helper 1 type immune response;signal transduction;cytokine-mediated signaling pathway;positive regulation of interferon-gamma production;interleukin-12-mediated signaling pathway;interleukin-23-mediated signaling pathway;positive regulation of activated T cell proliferation;positive regulation of memory T cell differentiation;cellular response to interferon-gamma;positive regulation of T-helper 17 type immune response;positive regulation of T-helper 17 cell lineage commitment
• Cellular component: plasma membrane;external side of plasma membrane;interleukin-12 receptor complex;receptor complex;interleukin-23 receptor complex
• Molecular function: cytokine receptor activity;interleukin-12 receptor binding;interleukin-12 receptor activity;cytokine binding;interleukin-23 binding;interleukin-23 receptor activity