IL12B

protein-coding

interleukin 12B, the group of Interleukins|Immunoglobulin like domain containing

Gene summary

This gene encodes a subunit of interleukin 12, a cytokine that acts on T and natural killer cells, and has a broad array of biological activities. Interleukin 12 is a disulfide-linked heterodimer composed of the 40 kD cytokine receptor like subunit encoded by this gene, and a 35 kD subunit encoded by IL12A. This cytokine is expressed by activated macrophages that serve as an essential inducer of Th1 cells development. This cytokine has been found to be important for sustaining a sufficient number of memory/effector Th1 cells to mediate long-term protection to an intracellular pathogen. Overexpression of this gene was observed in the central nervous system of patients with multiple sclerosis (MS), suggesting a role of this cytokine in the pathogenesis of the disease. The promoter polymorphism of this gene has been reported to be associated with the severity of atopic and non-atopic asthma in children. [provided by RefSeq, Jul 2008]

Previous symbols:
  • NKSF2

MANE transcript

NM_002187.3

Inheritance

AR

ClinVar variants

P:16U:95B:69

Top phenotype

Immunodeficiency 28; Immunodeficiency 29

gnomAD constraint

pLI —, LoF o/e 0.53

Max pathogenic AF

—

Genomic locus

chr5:159,314,780-159,330,863

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~16.1 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Mendelian susceptibility to mycobacterial diseases due to complete IL12B deficiencyDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013954

Submitter: Ambry Genetics

Mendelian susceptibility to mycobacterial diseases due to complete IL12B deficiencySUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0013954

Submitter: Orphanet

Mendelian susceptibility to mycobacterial diseases due to complete IL12B deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013954

Submitter: Labcorp Genetics (formerly Invitae)

Mendelian susceptibility to mycobacterial diseases due to complete IL12B deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013954

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Immunodeficiency 28; Immunodeficiency 29AR

Manifestation: Allergy/Immunology/Infectious

Intervention: Allergy/Immunology/Infectious

Rationale: Individuals may be susceptible to severe and recurrent infections, including adverse sequelae from BCG vaccination, and prophylaxis and early and aggressive treatment of infections may be beneficial

Refs: 9603732; 9789052; 11753820Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to IL12B variants in ClinVar

6 Conditions Cataloged
Mendelian susceptibility to mycobacterial diseases due to complete IL12B deficiencyTotal: 195
Inborn genetic diseasesTotal: 32
not providedTotal: 6
IL12B-related disorderTotal: 6
Autosomal recessive mendelian susceptibility to mycobacterial diseases due to a complete deficiencyTotal: 1
Inherited susceptibility to mycobacterial diseasesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002187.3. 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.

EffectPLPVUSLBBSum
synonymous
6
clinvar
59
clinvar
1
clinvar
66
missense
89
clinvar
7
clinvar
2
clinvar
98
nonsense
5
clinvar
2
clinvar
7
start loss
0
frameshift
5
clinvar
2
clinvar
7
splice donor/acceptor (+/-2bp)
2
clinvar
2
Total10695663180

Highest pathogenic variant AF is 0.00003965402

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_002187.3RefSeqNP_002178.26MANE Select
ENST00000231228.3EnsemblENSP00000231228.26MANE Select
ENST00000696750.1EnsemblENSP00000512849.13Standard
ENST00000696751.1EnsemblENSP00000512850.13Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Type I diabetes mellitus - Homo sapiens (human)
  • Pertussis - Homo sapiens (human)
  • Legionellosis - Homo sapiens (human)
  • Allograft rejection - Homo sapiens (human)
  • Jak-STAT signaling pathway - Homo sapiens (human)

Biological Process

  • positive regulation of T cell mediated cytotoxicity
  • positive regulation of defense response to virus by host
  • natural killer cell activation involved in immune response
  • positive regulation of T-helper 1 type immune response
  • positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target

Molecular Function

  • cytokine receptor activity
  • cytokine activity
  • interleukin-12 receptor binding
  • protein binding
  • growth factor activity

Cellular Component

  • extracellular region
  • extracellular space
  • endoplasmic reticulum lumen
  • cytosol
  • external side of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000231228
Coding exons
6
Length
16105
Individuals with no LoFs
125728
Homozygous LoFs
0
Heterozygous LoFs
19
Defined
125747
p
0.0000756
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.5671541750.8790.000009912154
Missense (PolyPhen)2141.5370.50558567
Synonymous0.5836672.30.9130.00000450612
Loss of Function1.81917.10.5277.41e-7210

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000120.00012rare
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian0.000110.00011rare
Finnish00.0absent
European (Non-Finnish)0.000120.00011rare
South Asian00.0absent
Other0.000330.00033rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Cytokine that can act as a growth factor for activated T and NK cells, enhance the lytic activity of NK/lymphokine- activated killer cells, and stimulate the production of IFN-gamma by resting PBMC. {ECO:0000269|PubMed:11114383}.;
Disease
DISEASE: Immunodeficiency 29 (IMD29) [MIM:614890]: 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. IMD29 is characterized by undetectable IL12B secretion from leukocytes. Affected individuals generally present with BCG disease after vaccination in childhood, and at least half also have Salmonella infection. Disease phenotype is relatively mild, and patients have a good prognosis. {ECO:0000269|PubMed:11753820, ECO:0000269|PubMed:9854038}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Psoriasis 11 (PSORS11) [MIM:612599]: A common, chronic inflammatory disease of the skin with multifactorial etiology. It is characterized by red, scaly plaques usually found on the scalp, elbows and knees. These lesions are caused by abnormal keratinocyte proliferation and infiltration of inflammatory cells into the dermis and epidermis. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.769

Intolerance Scores

LoFtool
0.690
RVIS EVS
0.44
RVIS percentile EVS
77.8

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.719

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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