CIITA

Chr 16p13.13

class II major histocompatibility complex transactivator

Aliases:: C2TA, NLRA
MANE:: ENST00000324288.14

OMIM: 600005 ↗NCBI: 4261 ↗Ensembl ↗

Annotations refreshed 1 month ago.

Predicted protein structure

AlphaFold predicted structure

CIITA · P33076

v62025-08-01

Predicted Aligned Error matrix for CIITA — diagonal shows residue index, colour shows pairwise prediction confidence (lower is better) — Predicted Aligned Error

Mean pLDDT

68.8/ 100

Low

1,130 residues

Confidence breakdown

Very high(≥ 90)30%
Confident(70–90)32%
Low(50–70)9%
Very low(< 50)30%

Open interactive 3D viewer

AlphaFold (Jumper et al., 2021) · CC BY 4.0

Clinical relevance (Genomics England PanelApp)

Diagnostic Grade (Green)

COVID-19 research
BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease
BIALLELIC, autosomal or pseudoautosomal

Disease associations (Open Targets)

Immunodeficiency by defective expression of HLA class 2
0.79
MHC class II deficiency
0.75
rheumatoid arthritis
0.43
melanoma
0.38
inflammatory bowel disease
0.38
lung carcinoma
0.37
gastric carcinoma
0.37
colon adenocarcinoma
0.37
cutaneous melanoma
0.37
hemangioblastoma
0.37

Score is the Open Targets composite evidence score (0-1). Higher = stronger gene-disease association.

Protein function (UniProt)

MHC class II transactivator

Essential for transcriptional activity of the HLA class II promoter; activation is via the proximal promoter (PubMed:16600381, PubMed:17493635, PubMed:7749984, PubMed:8402893, PubMed:40608405). Does not bind DNA (PubMed:16600381, PubMed:17493635, PubMed:7749984, PubMed:8402893). May act in a coactivator-like fashion through protein-protein interactions by contacting factors binding to the proximal MHC class II promoter, to elements of the transcription machinery, or both PubMed:8402893, PubMed:7749984, (PubMed:16600381, PubMed:17493635). Alternatively it may activate HLA class II transcription by modifying proteins that bind to the MHC class II promoter (PubMed:16600381, PubMed:17493635, PubMed:7749984, PubMed:8402893). Also mediates enhanced MHC class I transcription; the promoter element requirements for CIITA-mediated transcription are distinct from those of constitutive MHC class I transcription, and CIITA can functionally replace TAF1 at these genes. Activates CD74 transcription (PubMed:32855215). Exhibits intrinsic GTP-stimulated acetyltransferase activity (PubMed:11172716). Exhibits serine/threonine protein kinase activity: can phosphorylate the TFIID component TAF7, the RAP74 subunit of the general transcription factor TFIIF, histone H2B at 'Ser-37' and other histones (in vitro) (PubMed:24036077). Has antiviral activity against Ebola virus and coronaviruses, including SARS-CoV-2 (PubMed:32855215). Induces resistance by up-regulation of the p41 isoform of CD74, which blocks cathepsin-mediated cleavage of viral glycoproteins, thereby preventing viral fusion (PubMed:32855215)