IL12B
protein-codinginterleukin 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]
- NKSF2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~16.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0013954
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0013954
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0013954
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0013954
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to IL12B variants in ClinVar
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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 6 | 59 | 1 | 66 | ||
| missense | 89 | 7 | 2 | 98 | ||
| nonsense | 5 | 2 | 7 | |||
| start loss | 0 | |||||
| frameshift | 5 | 2 | 7 | |||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 10 | 6 | 95 | 66 | 3 | 180 |
Highest pathogenic variant AF is 0.00003965402
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002178.2 | 6 | MANE Select | |
| Ensembl | ENSP00000231228.2 | 6 | MANE Select | |
| Ensembl | ENSP00000512849.1 | 3 | Standard | |
| Ensembl | ENSP00000512850.1 | 3 | Standard |
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:
- 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-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.567 | 154 | 175 | 0.879 | 0.00000991 | 2154 |
| Missense (PolyPhen) | 21 | 41.537 | 0.50558 | 567 | ||
| Synonymous | 0.583 | 66 | 72.3 | 0.913 | 0.00000450 | 612 |
| Loss of Function | 1.81 | 9 | 17.1 | 0.527 | 7.41e-7 | 210 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00012 | 0.00011 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |