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Genetics Home Reference: your guide to understanding genetic conditions     A service of the U.S. National Library of Medicine®


The information on this page was automatically extracted from online scientific databases.

What is the official name of the RAG1 gene?

The official name of this gene is “recombination activating gene 1.”

RAG1 is the gene's official symbol. The RAG1 gene is also known by other names, listed below.

What is the normal function of the RAG1 gene?

From NCBI Gene (

The protein encoded by this gene is involved in activation of immunoglobulin V-D-J recombination. The encoded protein is involved in recognition of the DNA substrate, but stable binding and cleavage activity also requires RAG2. Defects in this gene can be the cause of several diseases. [provided by RefSeq, Jul 2008]

From UniProt (RAG1_HUMAN) (

Catalytic component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during V(D)J recombination. V(D)J recombination assembles a diverse repertoire of immunoglobulin and T-cell receptor genes in developing B and T-lymphocytes through rearrangement of different V (variable), in some cases D (diversity), and J (joining) gene segments. In the RAG complex, RAG1 mediates the DNA-binding to the conserved recombination signal sequences (RSS) and catalyzes the DNA cleavage activities by introducing a double-strand break between the RSS and the adjacent coding segment. RAG2 is not a catalytic component but is required for all known catalytic activities. DNA cleavage occurs in 2 steps: a first nick is introduced in the top strand immediately upstream of the heptamer, generating a 3'-hydroxyl group that can attack the phosphodiester bond on the opposite strand in a direct transesterification reaction, thereby creating 4 DNA ends: 2 hairpin coding ends and 2 blunt, 5'-phosphorylated ends. The chromatin structure plays an essential role in the V(D)J recombination reactions and the presence of histone H3 trimethylated at 'Lys-4' (H3K4me3) stimulates both the nicking and haipinning steps. The RAG complex also plays a role in pre-B cell allelic exclusion, a process leading to expression of a single immunoglobulin heavy chain allele to enforce clonality and monospecific recognition by the B-cell antigen receptor (BCR) expressed on individual B-lymphocytes. The introduction of DNA breaks by the RAG complex on one immunoglobulin allele induces ATM-dependent repositioning of the other allele to pericentromeric heterochromatin, preventing accessibility to the RAG complex and recombination of the second allele. In addition to its endonuclease activity, RAG1 also acts as a E3 ubiquitin-protein ligase that mediates monoubiquitination of histone H3. Histone H3 monoubiquitination is required for the joining step of V(D)J recombination. Mediates polyubiquitination of KPNA1.

How are changes in the RAG1 gene related to health conditions?

UniProt (RAG1_HUMAN) ( provides the following information about the RAG1 gene's known or predicted involvement in human disease.

Combined cellular and humoral immune defects with granulomas (CHIDG): Immunodeficiency disease with granulomas in the skin, mucous membranes, and internal organs. Other characteristics include hypogammaglobulinemia, a diminished number of T and B-cells, and sparse thymic tissue on ultrasonography. The disease is caused by mutations affecting the gene represented in this entry.

Severe combined immunodeficiency autosomal recessive T-cell-negative/B-cell-negative/NK-cell-positive (T(-)B(-)NK(+) SCID): A form of severe combined immunodeficiency (SCID), a genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and cell-mediated immunity, leukopenia, and low or absent antibody levels. Patients present in infancy recurrent, persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of T-cell-mediated cellular immunity due to a defect in T-cell development. The disease is caused by mutations affecting the gene represented in this entry.

Omenn syndrome (OS): Severe immunodeficiency characterized by the presence of activated, anergic, oligoclonal T-cells, hypereosinophilia, and high IgE levels. The disease is caused by mutations affecting the gene represented in this entry.

Alpha/beta T-cell lymphopenia, with gamma/delta T-cell expansion, severe cytomegalovirus infection and autoimmunity (T-CMVA): An immunological disorder characterized by oligoclonal expansion of TCR gamma/delta T-cells, TCR alpha/beta T-cell lymphopenia, severe, disseminated cytomegalovirus infection and autoimmune cytopenia. The disease is caused by mutations affecting the gene represented in this entry.

NCBI Gene ( lists the following diseases or traits (phenotypes) known or believed to be associated with changes in the RAG1 gene.
  • Alpha/beta T-cell lymphopenia with gamma/delta T-cell expansion, severe cytomegalovirus infection, and autoimmunity
  • Combined cellular and humoral immune defects with granulomas
  • Histiocytic medullary reticulosis
  • Severe immunodeficiency, autosomal recessive, T-cell negative, B-cell negative, NK cell-positive (, a catalog designed for genetics professionals and researchers, provides the following information about the RAG1 gene and its association with health conditions.

Where is the RAG1 gene located?

Cytogenetic Location: 11p13

Molecular Location on chromosome 11: base pairs 36,510,400 to 36,579,762

(Homo sapiens Annotation Release 107, GRCh38.p2) (NCBI (

The RAG1 gene is located on the short (p) arm of chromosome 11 at position 13.

The RAG1 gene is located on the short (p) arm of chromosome 11 at position 13.

More precisely, the RAG1 gene is located from base pair 36,510,400 to base pair 36,579,762 on chromosome 11.

See How do geneticists indicate the location of a gene? ( in the Handbook.

Where can I find additional information about RAG1?

You and your healthcare professional may find the following resources about RAG1 helpful.

You may also be interested in these resources, which are designed for genetics professionals and researchers.

What other names do people use for the RAG1 gene or gene products?

  • RAG-1
  • RNF74

See How are genetic conditions and genes named? ( in the Handbook.

What glossary definitions help with understanding RAG1?

allele ; antibody ; autoimmune ; autoimmunity ; autosomal ; autosomal recessive ; B-cells ; B-lymphocytes ; catalytic ; cell ; chromatin ; congenital ; deficiency ; DNA ; endonuclease ; expressed ; gene ; heterochromatin ; histone ; hydroxyl ; immunodeficiency ; immunoglobulin ; infection ; ligase ; lymphopenia ; Lys ; mucous ; protein ; rearrangement ; receptor ; recessive ; syndrome ; T-cells ; tissue ; ubiquitin ; ultrasonography

You may find definitions for these and many other terms in the Genetics Home Reference Glossary.


The resources on this site should not be used as a substitute for professional medical care or advice. Users seeking information about a personal genetic disease, syndrome, or condition should consult with a qualified healthcare professional. See How can I find a genetics professional in my area? ( in the Handbook.

Published: February 1, 2016