IL12A

interleukin 12A, the group of Interleukins

Basic information

Region (hg38): 3:159988834-159996019

Previous symbols: [ "NKSF1" ]

Links

ENSG00000168811 ∙ NCBI:3592 ∙ OMIM:161560 ∙ HGNC:5969 ∙ Uniprot:P29459 ∙ 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 IL12A gene.

• not provided (5 variants)
• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IL12A 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	2	3
missense			5	1	1	7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	2	3

Variants in IL12A

This is a list of pathogenic ClinVar variants found in the IL12A region.

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

Position	Type	Phenotype	Significance	ClinVar
3-159989073-C-T		not specified	Uncertain significance (Feb 28, 2023)
3-159989102-G-A		not specified	Likely benign (Dec 30, 2023)
3-159990236-C-A		not specified	Uncertain significance (Jul 06, 2021)
3-159990280-C-G		not specified	Uncertain significance (Jul 21, 2022)
3-159993053-G-A			Likely benign (Aug 01, 2018)
3-159993099-G-A		not specified	Uncertain significance (Dec 19, 2022)
3-159993586-T-A		not specified	Uncertain significance (Dec 09, 2023)
3-159993749-G-A		not specified	Uncertain significance (Aug 04, 2023)
3-159993805-A-G			Benign (Jul 19, 2018)
3-159993815-A-G		not specified	Uncertain significance (Oct 30, 2023)
3-159995428-G-A			Benign (Apr 01, 2023)
3-159995456-C-T			Likely benign (Aug 22, 2018)
3-159995457-G-A			Benign (Aug 08, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IL12A	protein_coding	protein_coding	ENST00000305579	7	7270

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0475	0.931	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.832	108	135	0.799	0.00000618	1667
Missense in Polyphen		30	41.919	0.71567		549
Synonymous	0.0849	50	50.8	0.985	0.00000237	492
Loss of Function	2.00	4	11.2	0.356	4.73e-7	142

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000180	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000336	0.0000327
Other	0.00	0.00

dbNSFP

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.
• Pathway: 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);Influenza A - Homo sapiens (human);Inflammatory bowel disease (IBD) - Homo sapiens (human);African trypanosomiasis - Homo sapiens (human);Amoebiasis - Homo sapiens (human);Malaria - Homo sapiens (human);Chagas disease (American trypanosomiasis) - Homo sapiens (human);Toll-like receptor signaling pathway - Homo sapiens (human);C-type lectin receptor signaling pathway - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Th1 and Th2 cell differentiation - Homo sapiens (human);Leishmaniasis - Homo sapiens (human);Toxoplasmosis - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Measles - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);RIG-I-like receptor signaling pathway - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);JAK-STAT-Core;Regulation of toll-like receptor signaling pathway;Allograft Rejection;Aryl Hydrocarbon Receptor Pathway;Vitamin D Receptor Pathway;Nuclear Receptors Meta-Pathway;Development and heterogeneity of the ILC family;Interleukin-10 signaling;Interleukin-4 and 13 signaling;PI3K-AKT-mTOR - VitD3 Signalling;no2-dependent il-12 pathway in nk cells;Toll-like Receptor Signaling Pathway;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;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Immune System;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;JAK STAT pathway and regulation;GPCR signaling-G alpha i;Interleukin-12 signaling;IL27-mediated signaling events;IL12-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.525

Intolerance Scores

• loftool: 0.152
• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.98

Haploinsufficiency Scores

• pHI: 0.0743
• hipred: N
• hipred_score: 0.212
• ghis: 0.367

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.983

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Il12a
• Phenotype: hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); neoplasm; respiratory system phenotype; immune system phenotype; skeleton phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: positive regulation of T cell mediated cytotoxicity;positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target;immune response;cell cycle arrest;cell population proliferation;response to virus;response to UV-B;regulation of signaling receptor activity;cell migration;cytokine-mediated signaling pathway;response to lipopolysaccharide;interferon-gamma production;negative regulation of interleukin-17 production;positive regulation of interferon-gamma production;positive regulation of natural killer cell activation;positive regulation of mononuclear cell proliferation;positive regulation of smooth muscle cell apoptotic process;T-helper 1 cell activation;interleukin-12-mediated signaling pathway;T-helper 1 cell cytokine production;positive regulation of T cell proliferation;positive regulation of tyrosine phosphorylation of STAT protein;defense response to protozoan;positive regulation of T cell differentiation;positive regulation of cell adhesion;positive regulation of natural killer cell mediated cytotoxicity;negative regulation of smooth muscle cell proliferation;positive regulation of lymphocyte proliferation;defense response to Gram-positive bacterium;positive regulation of NK T cell activation;interleukin-35-mediated signaling pathway;cellular response to lipopolysaccharide;extrinsic apoptotic signaling pathway;cellular response to virus;positive regulation of dendritic cell chemotaxis
• Cellular component: extracellular region;extracellular space;endoplasmic reticulum lumen;cell surface;late endosome lumen;interleukin-12 complex
• Molecular function: cytokine activity;interleukin-12 receptor binding;protein binding;growth factor activity;interleukin-12 beta subunit binding;interleukin-27 binding;protein heterodimerization activity