GENE REFERENCE / HGNC:9988

RFXAP

regulatory factor X associated protein

protein-coding gene13q13.3Gene information

What does this gene do?

The RFXAP gene provides instructions for making a protein called RFX associated protein (RFXAP). It 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 RFXAP is critical for the production of specialized immune proteins called MHC class II proteins from these genes.

The RFXAP protein is part of a group of proteins called the regulatory factor X (RFX) complex. This complex attaches to a specific region of DNA involved in the regulation of MHC class II gene activity. The RFXAP protein helps the complex attach to the correct region of DNA. The RFX complex attracts other necessary proteins to this region and helps turn on MHC class II gene transcription, allowing 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 RFX complex also appears to play a role in 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 RFX complex is able to help control 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 2023-06-15	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: 287
Submissions for variants in or overlapping this gene: 364
Submissions explicitly reporting this gene: 302
Alleles reported pathogenic / likely pathogenic: 31
VariationIDs with uncertain significance: 129
VariationIDs with conflicting classifications: 5

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 RFXAP?

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 31 alleles in RFXAP 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 RFXAP.

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

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