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CIITA

Synonyms
C2TA, CIITAIV, MHC2TA, NLRA
External resources
Summary
This gene encodes a protein with an acidic transcriptional activation domain, 4 LRRs (leucine-rich repeats) and a GTP binding domain. The protein is located in the nucleus and acts as a positive regulator of class II major histocompatibility complex gene transcription, and is referred to as the 'master control factor' for the expression of these genes. The protein also binds GTP and uses GTP binding to facilitate its own transport into the nucleus. Once in the nucleus it does not bind DNA but rather uses an intrinsic acetyltransferase (AT) activity to act in a coactivator-like fashion. Mutations in this gene have been associated with bare lymphocyte syndrome type II (also known as hereditary MHC class II deficiency or HLA class II-deficient combined immunodeficiency), increased susceptibility to rheumatoid arthritis, multiple sclerosis, and possibly myocardial infarction. Several transcript variants encoding different isoforms have been found for this gene.

Variant counts

The variants found in rare patients tested by 3billion are classified and counted according to ACMG guidelines. The variants with over 5% variant frequency in population genome databases ( gnomAD, dbSNP, etc) are excluded.

Pathogenic
9
Likely pathogenic
0
VUS
6,049
Likely benign
5,516
Benign
1,035

Patient phenotypes

Proportions of phenotypes among 9 patients carrying pathogenic or likely pathogenic variants on CIITA gene are displayed below.

Phenotype class
Patients in 3billion (%)
Abnormality of the musculoskeletal system
55.6%
Abnormality of head or neck
22.2%
Abnormality of limbs
22.2%
Abnormality of the integument
22.2%
Abnormality of the nervous system
22.2%
Abnormality of prenatal development or birth
11.1%
Abnormality of the ear
11.1%
Abnormality of the genitourinary system
11.1%
Abnormality of the respiratory system
11.1%
Abnormal cellular phenotype
0%
Abnormality of blood and blood-forming tissues
0%
Abnormality of metabolism homeostasis
0%
Abnormality of the breast
0%
Abnormality of the cardiovascular system
0%
Abnormality of the digestive system
0%
Abnormality of the endocrine system
0%
Abnormality of the eye
0%
Abnormality of the immune system
0%
Abnormality of the thoracic cavity
0%
Abnormality of the voice
0%
Constitutional symptom
0%
Growth abnormality
0%
Neoplasm
0%

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