GENE REFERENCE / HGNC:7067

CIITA

class II major histocompatibility complex transactivator

protein-coding gene16p13.13Gene information

What does this gene do?

The CIITA gene provides instructions for making a protein that primarily helps control the activity (transcription) of genes called major histocompatibility complex (MHC) class II genes. Transcription is the first step in the production of proteins, and CIITA is critical for the production of specialized immune proteins called MHC class II proteins from these genes. The CIITA protein coordinates various proteins to turn on MHC class II gene transcription and allow the production of MHC class II proteins.

MHC class II proteins are found on the surface of several types of immune cells, including white blood cells (lymphocytes) that are involved in immune reactions. These proteins play an important role in the body's immune response to foreign invaders, such as bacteria, viruses, and fungi. To help the body recognize and fight infections, MHC class II proteins bind to fragments of proteins (peptides) from foreign invaders so that other specialized immune system cells can interact with them. When these immune system cells recognize the peptides as harmful, they trigger the lymphocytes and other immune cells to launch immune responses to get rid of the foreign invaders.

The CIITA protein also appears to play a role in enhancing the transcription of MHC class I genes, which provide instructions for making immune system proteins called MHC class I proteins. Like MHC class II proteins, MHC class I proteins attach to peptides from foreign invaders and present them to specific immune system cells. These cells then attack the foreign invaders to rid them from the body. While the CIITA protein is able to help promote MHC class I gene activity, it is not the primary regulator of these genes. Other proteins play a more prominent role in their transcription.

Source: MedlinePlus, National Library of Medicine. Source publication: 2020-08-18. Source review: 2017-05.

ClinGen reviews

ClinGen reviews the evidence linking a particular gene to a condition. Each rating below describes the strength of that link. It does not classify a variant in your DNA file.

Condition	Inheritance	Evidence
MHC class II deficiencyMONDO:0008855 · Evaluated 2022-11-03	Autosomal recessive	DefinitiveSCID-CID Gene Curation Expert Panel

ClinVar records

These numbers show what has been submitted to ClinVar. They cannot tell you how likely you are to have a condition.

Submitted alleles: 1,965
Submissions for variants in or overlapping this gene: 2,776
Submissions explicitly reporting this gene: 2,707
Alleles reported pathogenic / likely pathogenic: 112
VariationIDs with uncertain significance: 697
VariationIDs with conflicting classifications: 58

The rows count different things: alleles, submissions or VariationIDs. Their categories can overlap, so do not add them together. Pathogenic/likely pathogenic counts exclude structural variants that merely overlap a gene. A dash in the source means “not reported,” not zero.

NCBI produces the gene-summary file each week using counts recorded at the start of the month. The numbers may differ from those on the live ClinVar website. Read the field definitions ↗

View this gene in ClinVar ↗

YOUR DNA FILE

Can your DNA file tell you about CIITA?

From a DNA test kit (such as 23andMe, AncestryDNA or MyHeritage). These kits check a fixed list of about 600,000 to 700,000 positions across your whole genome. ClinVar lists 112 alleles in CIITA reported as pathogenic or likely pathogenic. A kit checks only some of these positions, and often none of them.

From whole genome sequencing (a VCF file). Sequencing reads most of your genome. Your file lists the places where your DNA differs from the reference genome. Some regions are hard to sequence, including parts of some genes that have near-identical copies elsewhere, and a VCF file does not record which positions were read well.

If a variant is not in your file, that does not mean you don’t have it.

What BioDecode checks

BioDecode compares every variant in your file with ClinVar, on your own computer. For each match, it shows the ClinVar classification, the review status and the condition it was reported for. Your file is not uploaded.

A ClinVar classification applies to one particular variant and the condition it was reported for. It does not tell you about other variants in CIITA.

BioDecode cannot fill gaps in your test, diagnose a condition or replace clinical testing.

Buy BioDecode See a sample report →Check file compatibility →