HGNC Approved Gene Symbol: RAG1
SNOMEDCT: 307650006, 722067005;
Cytogenetic location: 11p12 Genomic coordinates (GRCh38): 11:36,510,353-36,579,762 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 11p12 | Alpha/beta T-cell lymphopenia with gamma/delta T-cell expansion, severe cytomegalovirus infection, and autoimmunity | 609889 | 3 | |
| Combined cellular and humoral immune defects with granulomas | 233650 | Autosomal recessive | 3 | |
| Omenn syndrome | 603554 | Autosomal recessive | 3 | |
| Severe combined immunodeficiency, B cell-negative | 601457 | Autosomal recessive | 3 |
RAG1 and RAG2 (179616) initiate the V(D)J recombination process, in which the variable (V), diversity (D), and joining (J) coding elements of the immunoglobulin (Ig) and T-cell receptor (TCR) genes are joined together to generate antigen-specific B- and T-cell receptors. Two molecules of RAG1 and 2 molecules of RAG2 form a heterotetramer that binds to recombination signal sequences (RSSs) flanking the V, D, and J genes and introduces double-strand breaks in the DNA, which are subsequently repaired by the nonhomologous end-joining DNA repair pathway. RAG1 contains the RNase H fold catalytic domain and regions that make direct contact with RSSs and is responsible for the enzymatic activity of the RAG complex. RAG2 promotes DNA binding by scanning the genome for enzymatic signatures characterized by histone-3 (H3; see 602810) trimethylated at lys4 (H3K4me3) and facilitates the cleavage functions of RAG1 (review by Bosticardo et al., 2021).
Schatz et al. (1989) isolated the RAG1 gene, which activates the V(D)J recombination when introduced into NIH 3T3 fibroblasts. Nucleotide sequencing of human and mouse RAG1 cDNA clones encode predicted 119-kD proteins of 1,043 and 1,040 amino acids, respectively, with 90% sequence identity. The RAG1 gene has been conserved between species that carry out the V(D)J recombination, and its pattern of expression correlates exactly with the pattern of expression of V(D)J recombinase activity. Oettinger et al. (1990) gave a corrected length of 6.6 kb for the RAG1 cDNA.
Schatz et al. (1989) raised the question of whether RAG1 activates the V(D)J recombination indirectly or whether it may encode the V(D)J recombinase itself. The scid mouse, caused by a recessive mutation on chromosome 16 of that species, has disruption of normal V(D)J recombination. Schatz et al. (1989) reported that Southern blots of DNA from a variety of somatic cell hybrids demonstrated that the murine equivalent of RAG1 does not map to chromosome 16, thus indicating that it is not the site of the mutation in the scid mouse. There is some reason to think that the scid gene does not encode the V(D)J recombinase because myeloid and fibroblastoid cells show an increased sensitivity to radiation-induced damage in that mutant mouse, suggesting that the defect is in a ubiquitously expressed factor involving both V(D)J recombination and the repair of chromosomal damage (Fulop and Phillips, 1990).
Formation of double-strand breaks at recombination signal sequences is an early step in V(D)J recombination. McBlane et al. (1995) showed that purified RAG1 and RAG2 proteins are sufficient to carry out this reaction. The cleavage reaction can be divided into 2 distinct steps, nicking and hairpin formation, each of which requires the presence of a signal sequence and both RAG proteins.
By site-directed mutagenesis of acidic amino acid residues in RAG1 and RAG2, Landree et al. (1999) and Kim et al. (1999) identified 3 RAG1 mutants that retained normal binding of recombination signal sequences but were catalytically inactive for both nicking and hairpin formation. The data suggested that 1 active site in RAG1 performs both of these steps and that at least 1 of these amino acid residues contacts and coordinates a metal ion, which is required for cleavage. The results also suggested that RAG1 contains most, if not all, of the active site of the RAG1/RAG2 V(D)J recombinase.
Yarnell Schultz et al. (2001) identified 2 RAG1 mutants, glu547 to gln (E547Q) and glu423 to gln (E423Q), that were proficient for DNA cleavage but severely defective for coding and signal joint formation, providing direct evidence that RAG1 is critical for joining in vivo and strongly suggesting that the postcleavage complex is important in end joining. The E423Q mutant was severely defective for both hairpin opening in vitro and coding joint formation in vivo. These data suggested that the hairpin opening activity of the RAG proteins plays an important physiologic role in V(D)J recombination.
Hikida et al. (1996) reported that RAG1 and RAG2 are expressed in mature mouse B cells after culture with interleukin-4 (147780) in association with costimuli (lipopolysaccharide and other cytokines). Reexpression was also detected in draining lymph nodes from immunized mice. Hikida et al. (1996) noted that previously reported studies had indicated that RAG1 and RAG2 were expressed only in immature B cells.
Immunoglobulin and T-cell receptor genes are assembled from component gene segments in developing lymphocytes by a site-specific recombination reaction which mediates V(D)J joining. Agrawal et al. (1998) showed that RAG1 and RAG2 are essential to this reaction. Together they form a transposase capable of excising a piece of DNA-containing recombination signals from a donor site and inserting it into a target DNA molecule. The products formed contain a short duplication of target DNA immediately flanking the transposed reactions. The results supported the theory that RAG1 and RAG2 were once components of a transposable element, and that the split nature of immunoglobulin and T-cell receptor genes derived from germline insertion of this element into an ancestral receptor gene soon after the evolutionary divergence of jawed and jawless vertebrates. Thus the repertoire of the human immune system may owe to 1 transposon insertion, which occurred 450 million years ago in an ancestor of the jawed vertebrates. Vertebrates seemed to have tamed this ancient transposon for generation of the immune repertoire. It was surprising when RAG1 and RAG2 were discovered (by Schatz and Oettinger working as graduate students in the laboratory of David Baltimore (Schatz et al., 1989)) to be located within such a small segment of the genome. This was a lucky circumstance since the selection system they used required that both be present in the fragment. The work of Agrawal et al. (1998) explained the reason for this close situation: they once had to fit in a small transposable element.
Like Agrawal et al. (1998), Hiom et al. (1998) concluded that the RAG-mediated V(D)J recombination system evolved from an ancient mobile DNA element. They suggested that repeated transposition may have promoted the expansion of the antigen receptor loci. They stated further that the inappropriate diversion of V(D)J rearrangement to a transpositional pathway may help explain certain types of DNA translocation associated with lymphatic tumors.
Roman and Baltimore (1996) presented genetic evidence that RAG1 is directly involved in the recognition of the DNA substrate. The RAG1 genomic locus was originally isolated by its ability to activate recombination in the fibroblast line 3TGR. 3TGR harbors an integrated retroviral recombination substrate that contains a neomycin (neo) resistance gene, which is dependent on inversion via V(D)J recombination for its transcriptional activation. Two murine RAG1 cDNAs, called M2 and M6 by them, were originally isolated by their group (Schatz et al., 1989), but only 1 of the clones (M2) encoded a protein that complemented recombination in 3TGR cells; M6 was inactive. Roman and Baltimore (1996) showed that the M6 cDNA contained a single amino acid substitution (H109L) in the RAG1 gene that rendered its activity sensitive to the sequence of the V(D)J coding region abutting the heptamer site in the recombination signal sequence. These results indicated to Roman and Baltimore (1996) that RAG1 interacts directly with DNA.
Yu et al. (1999) investigated the regulation of RAG1 and RAG2 in vivo with bacterial artificial chromosome (BAC) transgenes containing a fluorescent indicator. Coordinate expression of RAG1 and RAG2 in B and T cells was regulated by distinct genetic elements found on the 5-prime side of the RAG2 gene. This observation suggested a mechanism by which asymmetrically disposed cis DNA elements could influence the expression of the primordial transposon and thereby capture RAGs for vertebrate evolution.
During development of B and T cells, the RAG1/RAG2 protein complex cleaves DNA at conserved RSSs to initiate V(D)J recombination. RAG1/RAG2 also catalyzes transpositional strand transfer of RSS-containing substrates into target DNA to form branched DNA intermediates. Melek and Gellert (2000) showed that RAG1/RAG2 can resolve these intermediates by 2 pathways. RAG1/RAG2 catalyzes hairpin formation on target DNA adjacent to transposed RSS ends in a manner consistent with a model leading to chromosome translocations. Alternatively, disintegration removes transposed donor DNA from the intermediate. At high magnesium concentrations, such as those present in mammalian cells, disintegration is the favored pathway of resolution. The authors suggested that this may explain in part why RAG1/RAG2-mediated transposition does not occur at high frequency in cells.
Janeway (2001) reviewed the workings of the immune system in providing protection against infection. He discussed both innate immunity and adaptive immunity, and reviewed the source of adaptive immunity: invasion of a retroposon. Adaptive immunity only became possible after the acquisition of a retroposon that invaded the genome of an unknown organism many millions of years ago. It is thought that this organism had to have been a vertebrate, as only vertebrates have both of the elements of the retroposon: (1) the 2 genes that encode a site-specific recombinase, known as RAG1 and RAG2, and (2) the 2 sites that apparently were used by the retroposon to invade a member of the primordial immunoglobulin gene family, namely, the recognition signal sequences. These are short DNA sequences that are found adjacent to all Ig and T-cell receptor gene segments. One of these is made up of a heptamer-12-bp nonamer, and the other is made up of a heptamer-23-bp nonamer. These recognition signal sequences and the DNA that lies between them must be removed by the RAG1/RAG2 heterodimer to form 2 joints, one of which is religated to form a coding joint that encodes the variable exon of all immunoglobulins and T-cell receptors. Janeway (2001) stated that 'The invasion of a primordial Ig gene by a retroposon has only 'recently' been described, but the evidence for it is so strong that it almost has to be correct.` The site-directed recombinase, RAG1/RAG2, acts on germline gene segments to produce all antibody molecules and T-cell receptors of the adaptive immune system, as proven by the total inability of RAG1 and/or RAG2 knockout mice to rearrange their receptor gene segments.
Huye et al. (2002) mutated the 86 conserved basic amino acids of RAG1 to alanine and tested the mutant proteins for DNA binding, nicking, hairpin formation, and joining. They identified several of these amino acids outside the canonical RAG1 N-terminal DNA nonamer-binding domain that are located in the C terminus and are critical for DNA binding. Mutants of these residues retained the ability to interact with RAG2. Several step arrest mutants had defects in nicking or hairpin formation; the latter were centrally located. The authors also identified 4 C-terminal mutants defective specifically for joining. Analysis of the coding joints formed by some of these mutants revealed deletions and insertions resulting from aberrant hairpin opening, similar to the junctions found in scid mice. These scid junctions are deficient for the catalytic subunit of DNA-dependent protein kinase (PRKDC; 600899), suggesting that the RAG proteins and PRKDC perform overlapping functions in coding joint formation. Huye et al. (2002) observed 12 mutants with alterations that affected amino acids mutated in human inherited immunodeficiency syndromes, indicating that these residues are critical for recombination of the endogenous antigen receptor loci in developing lymphocytes.
Corneo et al. (2007) found that removing certain portions of murine Rag proteins revealed robust alternative nonhomologous end-joining (NHEJ) activity in NHEJ-deficient cells and some alternative joining activity even in wildtype cells. Corneo et al. (2007) proposed a 2-tier model in which the Rag proteins collaborate with NHEJ factors to preserve genomic integrity during V(D)J recombination.
Using chromatin immunoprecipitation analysis, Ji et al. (2010) demonstrated that mouse Rag protein binding was tightly regulated during lymphocyte development, focusing on a small region encompassing J and, where present, J-proximal D gene segments in IgH (see 147100), Igk (see 147200), Tcrb (see 186930), and Tcra (see 186880) loci. These regions, which the authors termed recombination centers, were rich in activating histone modifications and RNA polymerase II (see 180660). Rag2 bound broadly in the genome at sites with substantial trimethylation at lys4 of H3. In contrast, Rag1 binding was more specific, occurring primarily with recombination signal sequences (RSS) flanking V, D, and J gene segments. Ji et al. (2010) proposed that recombination centers are specialized sites of high local RAG concentration that facilitate RSS binding and synapsis and help regulate recombination order.
The ETV6/RUNX1 fusion gene (see 600618), found in 25% of childhood acute lymphoblastic leukemia cases (ALL; 613065), is acquired in utero but requires additional somatic mutations for overt leukemia. Papaemmanuil et al. (2014) used exome and low-coverage whole-genome sequencing to characterize secondary events associated with leukemic transformation in ETV6/RUNX1 ALL. RAG-mediated deletions emerged as the dominant mutational process, characterized by recombination signal sequence motifs near breakpoints, incorporation of nontemplated sequence at junctions, approximately 30-fold enrichment at promoters and enhancers of genes actively transcribed in B-cell development, and an unexpectedly high ratio of recurrent to nonrecurrent structural variants. Single-cell tracking showed that this mechanism is active throughout leukemic evolution, with evidence of localized clustering and reiterated deletions.
Crystal Structure
Kim et al. (2015) reported the crystal structure of the mouse RAG1-RAG2 complex at 3.2-angstrom resolution. The 230-kD RAG1-RAG2 heterotetramer is Y-shaped, with the amino-terminal domains of the 2 RAG1 chains forming an intertwined stalk. Each RAG1-RAG2 heterodimer composes 1 arm of the Y, with the active site in the middle and RAG2 at its tip. The RAG1-RAG2 structure rationalizes more than 60 mutations identified in immunodeficient patients, as well as a large body of genetic and biochemical data.
Oettinger et al. (1992) mapped the RAG1 and RAG2 loci to 11p by Southern analysis of hybrid cell lines derived from patients with the WAGR syndrome (194070) and from mutagenized cell hybrids selected for deletions in chromosome 11. The RAG locus defined a new interval of human 11p which was not known to contain any genetically mapped human disease. Guided by the localization of the human genes, they mapped the homologous loci to mouse chromosome 2. Sherrington et al. (1992) confirmed the assignment of the RAG1 and RAG2 genes to human 11p13. The results of study of a somatic cell hybrid panel placed the RAG1 gene near CD44 and proximal to CAT. They pointed out that these recombinase-activating genes are thus not linked to ataxia-telangiectasia complementation groups A, C, or D, which have been mapped to the region 11q22-q23, and are presumably not directly responsible for the phenotype of that disorder (see 208900). Ichihara et al. (1992) mapped both RAG1 and RAG2 to 11p13-p12 by fluorescence in situ hybridization.
Schwarz et al. (1996) reported that patients with severe combined immunodeficiency can be divided into those with B lymphocytes (T-negative, B-positive SCID) and those without them (T-negative, B-negative SCID; 601457). They searched for RAG1 and RAG2 mutations in B-negative SCID patients through the use of SSCP analysis with primer cassettes overlapping the entire RAG1 and RAG2 coding regions. Six of 14 B-negative SCID patients were found to carry mutations of the recombinase activating genes. Mutations resulted in a functional inability to form antigen receptors through genetic recombination. In 4 families, 4 B-negative SCID patients exhibited an altered migration pattern for RAG1 amplimers. They identified 2 missense mutations (179615.0001 and 179615.0004) and 2 nonsense mutations (179615.0002 and 179615.0003) in RAG1. In 1 case there was a paternal deletion which encompassed the RAG1 and RAG2 loci on chromosome 11p13. Transient transfection assays revealed that the SCID-associated RAG1 and RAG2 mutations exhibited either a complete loss or a marked reduction of V(D)J recombination activity. The mutations were not detected in B+ SCID patients or in 35 healthy subjects.
Villa et al. (1998) reported that patients with Omenn syndrome (603554), a severe immunodeficiency characterized by the presence of activated, anergic, oligoclonal T cells, hypereosinophilia, and high IgE levels, have missense mutations in either the RAG1 or RAG2 genes that result is partial activity of the 2 proteins. Two of the amino acid substitutions map within the RAG1 homeodomain and decrease DNA binding activity, while 3 others lower the efficiency of RAG1/RAG2 interaction. These findings provided evidence indicating that the immunodeficiency manifested in patients with Omenn syndrome arises from mutations that decrease the efficiency of V(D)J recombination.
Santagata et al. (2000) reported 7 patients with Omenn syndrome and a novel class of genetic lesions: frameshift mutations within the 5-prime coding region of RAG1. They demonstrated in transient expression experiments that these frameshift deletion alleles remain partially functional for both deletional and inversional recombination. This explained the partial rearrangement phenotype observed in these patients. The rearrangement activity is mediated by truncated RAG1 proteins that are generated by alternative ATG initiator codon usage 3-prime to the frameshift deletion and that demonstrate improper cellular localization. These results suggested a novel mechanism for the development of immunodeficiency in a subset of Omenn syndrome patients.
Corneo et al. (2001) identified the same RAG1 mutations (179615.0010; 179615.0015) in patients with Omenn syndrome and T-, B- SCID. The findings suggested that an additional factor was required for the Omenn syndrome phenotype.
Tabori et al. (2004) performed mutation analyses of PCR products of the RAG1 and RAG2 genes in 6 cases of T-, B- SCID and 8 cases of Omenn syndrome. Consanguinity was reported in 7 of the 14 families. None of the patients had a mutation in the RAG1 gene, but Tabori et al. (2004) found 4 missense mutations in the RAG2 gene in 6 of 8 Omenn syndrome patients and in 4 of 6 SCID patients (see 179616.0007).
De Villartay et al. (2005) reported 4 unrelated infants born to first cousins who presented with a novel immunodeficiency consisting of alpha/beta T-cell lymphopenia with gamma/delta T-cell expansion, severe cytomegalovirus (CMV) infection, and autoimmunity (609889). They identified homozygous mutations in the RAG1 gene (e.g., 179615.0017) in all 4 patients. De Villartay et al. (2005) concluded that hypomorphic RAG1 mutations result in residual RAG1 activity and are compatible with the presence of both B and T lymphocytes. They suggested that the immunologic phenotypes associated with RAG1 mutations are dependent on both genetic background and the microbial environment.
In 3 children with T-, B-, NK+ SCID from 2 related families of Athabascan-speaking Dine Indians from the Canadian Northwest Territories, Xiao et al. (2009) identified homozygosity for a missense mutation in the RAG1 gene (179615.0023).
Yu et al. (2014) performed deep sequencing on complementarity-determining region-3 (CDR3) of T-cell receptor (TCR)-beta (see 186930) in CD4 (186940)-positive and CD8 (see 186910)-positive T cells from 2 patients with autoimmunity and/or granulomatous disease, but not severe immunodeficiency, caused by RAG1 or IL2RG (308380) mutations; 5 patients with Omenn syndrome caused by RAG1 or RAG2 mutations; 2 patients with Omenn syndrome-like phenotypes caused by a ZAP70 (176947) mutation (see 269840) or by atypical DiGeorge syndrome (188400); and 4 healthy controls. They found that patients with Omenn syndrome due to RAG1 or RAG2 mutations had poor TCR-beta diversity compared with controls and patients with Omenn syndrome not due to RAG1 or RAG2 mutations. The 2 patients with RAG1 or IL2RG mutations associated with autoimmunity and granulomatous disease did not have diminished diversity, but instead had skewed V-J pairing and CDR3 amino acid use. Yu et al. (2014) concluded that RAG enzymatic function may be necessary for normal CDR3 junctional diversity and that aberrant TCR generation, but not numeric diversity, may contribute to immune dysregulation in patients with hypomorphic forms of SCID.
Mombaerts et al. (1992) introduced a mutation in the V(D)J recombination activating gene RAG1 into the germline of mice via gene targeting in embryonic stem cells. They found that such mice had small lymphoid organs that did not contain mature B and T lymphocytes. The phenotype was that of 'nonleaky' scid mice. Although RAG1 expression had been reported in the central nervous system of the mouse, no obvious neuroanatomical or behavioral abnormalities were found in the RAG1-deficient mice.
Wienholds et al. (2002) generated viable and fertile Rag1-deficient zebrafish using chemical mutagenesis and reverse genetics. They noted that their cryopreserved sperm bank could also be a resource for mutants of most zebrafish genes.
Khiong et al. (2007) identified an apparently healthy female C57BL/10 mouse with an abnormally high percentage of memory-phenotype Cd8 (see 186910)-positive T lymphocytes. Nearly 25% of F2 offspring of F1 intercrossed mice had the same phenotype, which the authors termed MM for 'memory mutant,' indicating autosomal recessive inheritance. Khiong et al. (2007) identified a spontaneous point mutation in the Rag1 gene in MM mice that caused an arg972-to-glu (R972E) substitution in the core domain of the protein. The R972E substitution reduced Rag1 rearranging activity, but did not cause loss of the Rag1 protein. T- and B-cell development was blocked in MM mice at the Cd4 (186940)/Cd8 double-negative-3 and Cd43 (SPN; 182160)-positive/B220(med) (PTPRC; 151460) stages, respectively. MM mice had elevated serum IgE, IgG, and IgM, but not IgA, as well as eosinophilia and reduced lymphocyte numbers. They also displayed erythroderma, hepatosplenomegaly, and excess Cd4-positive T cells. Khiong et al. (2007) concluded that the MM mouse is a model of Omenn syndrome.
Giblin et al. (2009) generated a knockin mouse model with a hypomorphic ser723-to-cys (S723C) mutation in Rag1. The S723C mutant mice had impaired lymphocyte development and decreased V(D)J rearrangements. In contrast with Rag1 -/- mice, the S723C hypomorph resulted in aberrant double-strand breaks within loci undergoing rearrangement. The S723C mutation predisposed mice to thymic lymphomas associated with chromosomal translocations in a p53 (191170) mutant background. Heterozygosity for the mutant allele accelerated age-associated immune system dysfunction. Giblin et al. (2009) concluded that aberrant RAG1/RAG2 activity is implicated in lymphoid tumor development and premature immunosenescence.
Blanquet et al. (1992) had determined by in situ hybridization that the RAG1 gene is located in the 14q21.3-q22.2 region. This assignment must have been in error; possibly the probe used was not in fact from that gene (Oettinger, 1993).
Schwarz et al. (1996) found that a patient with B-negative SCID (601457) was compound heterozygous for a glu722-to-lys (E722K) missense mutation and a glu774-to-ter (E774X; 179615.0002) nonsense mutation in the RAG1 gene. She had inherited the missense mutation (caused by a 2276G-A transition) from her healthy mother and the nonsense mutation (caused by a 2432G-T transversion) from her healthy father.
For discussion of the glu774-to-ter (E774X) mutation in the RAG1 gene that was found in compound heterozygous state in a patient with B-negative SCID (601457) by Schwarz et al. (1996), see 179615.0001.
Schwarz et al. (1996) identified a B-negative SCID (601457) patient who was homozygous for a tyr938-to-ter (Y938X) nonsense mutation in the RAG1 gene. The nonsense mutation resulted from a 2926T-G transversion.
Schwarz et al. (1996) identified a patient with B-negative SCID (601457) who inherited an ala156-to-val substitution (A156V) in the RAG1 gene and an arg220-to-gln mutation in the RAG2 gene (179616.0002) from her mother. The A156V substitution resulted from a 579C-T transition. From her father she inherited a deletion that encompassed both the RAG1 and RAG2 loci. When transiently transfected into a human fibroblast cell line and assayed for recombination efficiency, the A156V mutant RAG1 gene gave recombination efficiencies similar to those of wildtype RAG1, suggesting that the mutation is a functional polymorphism.
Villa et al. (1998) found an arg561-to-his (R561H) mutation in homozygous state in a patient with Omenn syndrome (603554). This mutation occurs in a domain implicated in RAG1/RAG2 interaction.
Villa et al. (1998) found an arg396-to-cys (R396C) mutation in heterozygous state in a patient with Omenn syndrome (603554). This mutation occurs in the homeodomain of RAG1.
Villa et al. (1998) found a tyr912-to-cys (Y912C) mutation in heterozygous state in a patient with Omenn syndrome (603554). This mutation occurs in the active core of RAG1.
Villa et al. (1998) found an arg396-to-his (R396H) mutation in heterozygous state in a patient with Omenn syndrome (603554). This mutation occurs in the homeodomain of RAG1.
Villa et al. (1998) found an asp429-to-gly (D429G) mutation in heterozygous state in a patient with Omenn syndrome (603554). This mutation occurs in the homeodomain of RAG1.
Villa et al. (1998) identified a heterozygous arg561-to-cys (R561C) mutation in a patient with Omenn syndrome (603554). This mutation occurs in a domain implicated in RAG1/RAG2 interaction.
In a patient with T-, B- SCID (601457), Corneo et al. (2001) identified homozygosity for the R561C mutation. The findings suggested that an additional factor was required for the Omenn syndrome phenotype.
Villa et al. (1998) found an arg737-to-his (R737H) substitution in the heterozygous state in a patient with Omenn syndrome (603554). This mutation occurs in the active core of RAG1.
Villa et al. (1998) found a deletion of 13 nucleotides of RAG1 cDNA in heterozygous state in a patient with Omenn syndrome (603554). This mutation results in a truncated protein.
Villa et al. (1998) found a deletion of 2 nucleotides of RAG1 cDNA in heterozygous state in a patient with Omenn syndrome (603554). This mutation results in a truncated protein.
Santagata et al. (2000) demonstrated that a 2-bp deletion (AA) at nucleotides 368 and 369 results in a frameshift at proline-85 and addition of 32 amino acids before a stop. In 1 patient the deletion was combined in compound heterozygous state with the D429G missense mutation (179615.0009); in another patient it was combined with the E722K (179615.0001) missense mutation. In yet another patient the 2-bp deletion was present in homozygous state.
De Villartay et al. (2005) identified the RAG1 368AA deletion in homozygous state in a Turkish child of consanguineous parents who presented with severe, persistent cytomegalovirus infection, anti-red blood cell antibody-induced anemia, a high percentage of gamma/delta T cells, and a low percentage of alpha/beta T cells (609889).
One of the 7 patients with Omenn syndrome (603554) in whom Santagata et al. (2000) found N-terminal RAG1 frameshift mutations with internal methionine usage leading to partial V(D)J recombination activity was homozygous for a 1-bp deletion (A) at nucleotide 887 of the RAG1 gene, resulting in a frameshift at ser258 and the addition of 4 amino acids before a stop.
In 3 patients with Omenn syndrome (603554) and 1 patient with T-, B- SCID (601457), Corneo et al. (2001) identified a 1-bp deletion in the RAG1 gene (631delT). The findings suggested that an additional factor was required for the Omenn syndrome phenotype.
De Villartay et al. (2005) identified the RAG1 631delT mutation in homozygous state in an Algerian infant of consanguineous parents who presented with severe, persistent cytomegalovirus infection, low lymphocyte counts, a high percentage of gamma/delta T cells, and a low percentage of alpha/beta T cells (609889). Unlike other infants presenting with this phenotype, the infant with the 631delT mutation had no detectable autoimmunity.
De Villartay et al. (2005) identified a C-to-T transition at nucleotide 2633 in the RAG1 gene, resulting in an arg841-to-trp (R841W) substitution, in a child of consanguineous parents. The infant presented with severe, persistent cytomegalovirus infection, anti-red blood cell antibody-induced anemia, antinuclear antibodies, a high percentage of gamma/delta T cells, and a low percentage of alpha/beta T cells (609889). De Villartay et al. (2005) noted that the same mutation in heterozygous state was reported by Villa et al. (2001) in a patient with an atypical form of severe combined immunodeficiency (601457)/Omenn syndrome (603544).
De Villartay et al. (2005) identified a homozygous A-to-C transversion at nucleotide 3054 in the RAG1 gene, resulting in a gln981-to-pro (Q981P) substitution in the core domain of the protein, in a Moroccan child of consanguineous parents. The infant presented with severe, persistent cytomegalovirus infection, anti-red blood cell antibody-induced anemia, antineutrophil antibody-induced neutropenia, antinuclear antibodies, a high percentage of gamma/delta T cells, and a low percentage of alpha/beta T cells (609889).
In a child with combined cellular and humoral immune defects associated with granulomas (CCHIDG; 233650), Schuetz et al. (2008) identified compound heterozygosity for mutations in the RAG1 gene. The maternal allele carried an arg314-to-trp (R314W) substitution in the ubiquitin ligase portion of the protein, and the paternal allele carried 2 mutations in cis: arg507-to-trp (R507W; 179615.0019) and arg737-to-his (R737H; 179615.0011), both in the catalytic core of the protein. The patient presented at age 2.5 years with multiple facial papulonodular lesions composed of epithelioid cells with a strong lymphocytic infiltrate consistent with noninfectious granulomas. Extensive laboratory evaluation showed profound hypogammaglobulinemia, decreased T cells, and defective T-cell function. Bone marrow transplant was successful. In vitro functional expression studies showed that the mutant proteins had significantly impaired function. Schuetz et al. (2008) concluded that the relatively late onset and low incidence of repeated infections observed in this patient reflected a low level of residual RAG1 activity.
For discussion of the arg507-to-trp (R507W) and arg737-to-his (R737H) mutations in the RAG1 gene that were found in compound heterozygous state in a patient with combined cellular and humoral immune defects associated with granulomas (CCHIDG; 233650) by Schuetz et al. (2008), see 179615.0018.
R737H has been identified in the heterozygous state in another unrelated patient (see 179615.0011).
In a child with combined cellular and humoral immune defects associated with granulomas (CCHIDG; 233650), Schuetz et al. (2008) identified compound heterozygosity for 2 mutations in the RAG1 gene: arg778-to-gln (R778Q) and arg975-to-trp (R975W; 179615.0021). The patient developed severe infections in infancy and later developed skin, tongue, and lung lesions consistent with noninfectious granulomas. Immunophenotyping showed low numbers of B and T cells. In vitro functional expression studies showed that the mutant proteins had significantly impaired function.
For discussion of the arg975-to-trp (R975W) mutation in the RAG1 gene that was found in compound heterozygous state in a patient with combined cellular and humoral immune defects associated with granulomas (CCHIDG; 233650) by Schuetz et al. (2008), see 179615.0020.
In a 3-month-old patient with Omenn syndrome (603554), Villa et al. (2001) identified a homozygous G-to-A transition at nucleotide 1095 of the RAG1 gene, resulting in a cys328-to-tyr (C328Y) substitution.
Simkus et al. (2007) explored the biochemical defects resulting from the C328Y mutation in the RING finger/ubiquitin ligase domain of RAG1 by expressing the equivalent mutation, C325Y, in full-length mouse Rag1. The C325Y mutation led to a 50-fold reduction in Rag1 recombination activity in cultured pro-B cells, even though its expression and nuclear localization were comparable to the wildtype protein. Ubiquitin ligase activity of the purified Rag1 RING finger domain with the C325Y mutation was severely abrogated, and the tertiary structure of the domain was altered. Substitution at an adjacent site within the Rag1 RING finger, pro326 to gly, also abrogated ubiquitin ligase activity and impaired recombination activity, but it had a less severe effect on protein folding. Simkus et al. (2007) concluded that correct folding of RAG1 RING finger domain is required for normal V(D)J recombination.
In 3 children with T-, B-, NK+, SCID (601457) from 2 related families of Athabascan-speaking Dine Indians from the Canadian Northwest Territories, Xiao et al. (2009) identified homozygosity for a 2438C-T transition in the RAG1 gene, resulting in an arg776-to-trp (R776W) substitution at a highly conserved residue in a C-terminal motif important for DNA binding and dimerization. Both sets of parents were heterozygous for the mutation, as was an unaffected sib. EGFP-based assays demonstrated impaired activity of the RAG1 mutant in V(D)J recombination, and overexpression of wildtype RAG1 in patient fibroblasts complemented V(D)J recombination, with recovery of both coding and signal joint formation.
In a boy with destructive midline granulomatous disease of the head and neck (CCHIDG; 233650), De Ravin et al. (2010) identified compound heterozygosity for 2 mutations in the RAG1 gene: a 1566G-T transversion, resulting in a trp522-to-cys (W522C) substitution, and a 1-bp deletion (1621delC; 179615.0025), resulting in a frameshift and premature termination after 30 novel residues. Each unaffected parent was heterozygous for 1 of the mutations. The patient had a complicated medical history. He had a history of myasthenia gravis with thymectomy at age 10 years, and a history of recurrent ear and sinus infections. The thymus showed dysplastic features and absence of autoimmune regulator, indicating a defect in thymocyte maturation. Laboratory studies showed a decrease of IgG subclasses 2 and 4 and mild CD8+ T cell lymphopenia, whereas CD3+ T cells, CD19+ B cells, and NK cells were normal. He was treated for Wegener granulomatosis with chemotherapeutic agents, but developed severe lymphopenia and continued to have relapses of noninfectious granulomas. In vitro studies showed dysregulated cellular inflammatory responses to various stimuli, including increased production of IL1B (147720) and IL8 (146930). Functional studies showed that the W522C mutant had about 50% residual RAG1 activity, but the deletion mutation had no activity. An older sister had autoimmune cytopenias and antinuclear antibody-positive collagen vascular disease, with death at age 5 years. De Ravin et al. (2010) concluded that the proband had a phenotypic variant of RAG1 deficiency, with some residual enzyme activity being responsible for the later presentation and milder phenotype. The authors suggested a dysregulation of the inflammatory response to environmental antigens in this patient.
For discussion of the 1-bp deletion in the RAG1 gene (1621delC) that was found in compound heterozygous state in a patient with destructive midline granulomatous disease of the head and neck (CCHIDG; 233650) by De Ravin et al. (2010), see 179615.0024.
Agrawal, A., Eastman, Q. M., Schatz, D. G. Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 394: 744-751, 1998. [PubMed: 9723614] [Full Text: https://doi.org/10.1038/29457]
Blanquet, V., Turleau, C., Goossens, M., Besmond, C. Assignment of the human recombination activating gene 1 (RAG1) to the 14q21.3-q22.2 region. Genomics 13: 488-489, 1992. [PubMed: 1612612] [Full Text: https://doi.org/10.1016/0888-7543(92)90282-w]
Bosticardo, M., Pala, F., Notarangelo, L. D. RAG deficiencies: recent advances in disease pathogenesis and novel therapeutic approaches. Europ. J. Immun. 51: 1028-1038, 2021. [PubMed: 33682138] [Full Text: https://doi.org/10.1002/eji.202048880]
Corneo, B., Moshous, D., Gungor, T., Wulffraat, N., Philippet, P., Le Deist, F., Fischer, A., de Villartay, J.-P. Identical mutations in RAG1 or RAG2 genes leading to defective V(D)J recombinase activity can cause either T-B-severe combined immune deficiency or Omenn syndrome. Blood 97: 2772-2776, 2001. [PubMed: 11313270] [Full Text: https://doi.org/10.1182/blood.v97.9.2772]
Corneo, B., Wendland, R. L., Deriano, L., Cui, X., Klein, I. A., Wong, S.-Y., Arnal, S., Holub, A. J., Weller, G. R., Pancake, B. A., Shah, S., Brandt, V. L., Meek, K., Roth, D. B. Rag mutations reveal robust alternative end joining. Nature 449: 483-486, 2007. [PubMed: 17898768] [Full Text: https://doi.org/10.1038/nature06168]
De Ravin, S. S., Cowen, E. W., Zarember, K. A., Whiting-Theobald, N. L., Kuhns, D. B., Sandler, N. G., Douek, D. C., Pittaluga, S., Poliani, P. L., Lee, Y. N., Notarangelo, L. D., Wang, L., Alt, F. W., Kang, E. M., Milner, J. D., Niemela, J. E., Fontana-Penn, M., Sinal, S. H., Malech, H. L. Hypomorphic Rag mutations can cause destructive midline granulomatous disease. Blood 116: 1263-1271, 2010. [PubMed: 20489056] [Full Text: https://doi.org/10.1182/blood-2010-02-267583]
de Villartay, J.-P., Lim, A., Al-Mousa, H., Dupont, S., Dechanet-Merville, J., Coumau-Gatbois, E., Gougeon, M.-L., Lemainque, A., Eidenschenk, C., Jouanguy, E., Abel, L., Casanova, J.-L., Fischer, A., Le Deist, F. A novel immunodeficiency associated with hypomorphic RAG1 mutations and CMV infection. J. Clin. Invest. 115: 3291-3299, 2005. [PubMed: 16276422] [Full Text: https://doi.org/10.1172/JCI25178]
Fulop, G. M., Phillips, R. A. The scid mutation in mice causes a general defect in DNA repair. Nature 347: 479-482, 1990. [PubMed: 2215662] [Full Text: https://doi.org/10.1038/347479a0]
Giblin, W., Chatterji, M., Westfield, G., Masud, T., Theisen, B., Cheng, H.-L., DeVido, J., Alt, F. W., Ferguson, D. O., Schatz, D. G., Sekiguchi, J. Leaky severe combined immunodeficiency and aberrant DNA rearrangements due to a hypomorphic RAG1 mutation. Blood 113: 2965-2975, 2009. [PubMed: 19126872] [Full Text: https://doi.org/10.1182/blood-2008-07-165167]
Hikida, M., Mori, M., Takai, T., Tomochika, K., Hamatani, K., Ohmori, H. Reexpression of RAG-1 and RAG-2 genes in activated mature mouse B cells. Science 274: 2092-2094, 1996. [PubMed: 8953042] [Full Text: https://doi.org/10.1126/science.274.5295.2092]
Hiom, K., Melek, M., Gellert, M. DNA transposition by the RAG1 and RAG2 proteins: a possible source of oncogenic translocations. Cell 94: 463-470, 1998. [PubMed: 9727489] [Full Text: https://doi.org/10.1016/s0092-8674(00)81587-1]
Huye, L. E., Purugganan, M. M., Jiang, M.-M., Roth, D. B. Mutational analysis of all conserved basic amino acids in RAG-1 reveals catalytic, step arrest, and joining-deficient mutants in the V(D)J recombinase. Molec. Cell. Biol. 22: 3460-3473, 2002. [PubMed: 11971977] [Full Text: https://doi.org/10.1128/MCB.22.10.3460-3473.2002]
Ichihara, Y., Hirai, M., Kurosawa, Y. Sequence and chromosome assignment to 11p13-p12 of human RAG genes. Immun. Lett. 33: 277-284, 1992. [PubMed: 1428003] [Full Text: https://doi.org/10.1016/0165-2478(92)90073-w]
Janeway, C. A., Jr. How the immune system works to protect the host from infection: a personal view. Proc. Nat. Acad. Sci. 98: 7461-7468, 2001. [PubMed: 11390983] [Full Text: https://doi.org/10.1073/pnas.131202998]
Ji, Y., Resch, W., Corbett, E., Yamane, A., Casellas, R., Schatz, D. G. The in vivo pattern of binding of RAG1 and RAG2 to antigen receptor loci. Cell 141: 419-431, 2010. Note: Erratum: Cell 143: 170 only, 2010. [PubMed: 20398922] [Full Text: https://doi.org/10.1016/j.cell.2010.03.010]
Khiong, K., Murakami, M., Kitabayashi, C., Ueda, N., Sawa, S., Sakamoto, A., Kotzin, B. L., Rozzo, S. J., Ishihara, K., Verella-Garcia, M., Kappler, J., Marrack, P., Hirano, T. Homeostatically proliferating CD4+ T cells are involved in the pathogenesis of an Omenn syndrome murine model. J. Clin. Invest. 117: 1270-1281, 2007. [PubMed: 17476359] [Full Text: https://doi.org/10.1172/JCI30513]
Kim, D. R., Dai, Y., Mundy, C. L., Yang, W., Oettinger, M. A. Mutations of acidic residues in RAG1 define the active site of the V(D)J recombinase. Genes Dev. 13: 3070-3080, 1999. [PubMed: 10601033] [Full Text: https://doi.org/10.1101/gad.13.23.3070]
Kim, M.-S., Lapkouski, M., Yang, W., Gellert, M. Crystal structure of the V(D)J recombinase RAG1-RAG2. Nature 518: 507-511, 2015. [PubMed: 25707801] [Full Text: https://doi.org/10.1038/nature14174]
Landree, M. A., Wibbenmeyer, J. A., Roth, D. B. Mutational analysis of RAG1 and RAG2 identifies three catalytic amino acids in RAG1 critical for both cleavage steps of V(D)J recombination. Genes Dev. 13: 3059-3069, 1999. [PubMed: 10601032] [Full Text: https://doi.org/10.1101/gad.13.23.3059]
McBlane, J. F., van Gent, D. C., Ramsden, D. A., Romeo, C., Cuomo, C. A., Gellert, M., Oettinger, M. A. Cleavage at a V(D)J recombination signal requires only RAG1 and RAG2 proteins and occurs in two steps. Cell 83: 387-395, 1995. [PubMed: 8521468] [Full Text: https://doi.org/10.1016/0092-8674(95)90116-7]
Melek, M., Gellert, M. RAG1/2-mediated resolution of transposition intermediates: two pathways and possible consequences. Cell 101: 625-633, 2000. [PubMed: 10892649] [Full Text: https://doi.org/10.1016/s0092-8674(00)80874-0]
Mombaerts, P., Iacomini, J., Johnson, R. S., Herrup, K., Tonegawa, S., Papaioannou, V. E. RAG-1-deficient mice have no mature B and T lymphocytes. Cell 68: 869-877, 1992. [PubMed: 1547488] [Full Text: https://doi.org/10.1016/0092-8674(92)90030-g]
Oettinger, M. A., Schatz, D. G., Gorka, C., Baltimore, D. RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science 248: 1517-1523, 1990. [PubMed: 2360047] [Full Text: https://doi.org/10.1126/science.2360047]
Oettinger, M. A., Stanger, B., Schatz, D. G., Glaser, T., Call, K., Housman, D., Baltimore, D. The recombination activating genes, RAG1 and RAG2, are on chromosome 11p in humans and chromosome 2p in mice. Immunogenetics 35: 97-101, 1992. [PubMed: 1735560] [Full Text: https://doi.org/10.1007/BF00189518]
Oettinger, M. A. Personal Communication. Boston, Mass. 1/15/1993.
Papaemmanuil, E., Rapado, I., Li, Y., Potter, N. E., Wedge, D. C., Tubio, J., Alexandrov, L. B., Van Loo, P., Cooke, S. L., Marshall, J., Martincorena, I., Hinton, J., and 25 others. RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia. Nature Genet. 46: 116-125, 2014. [PubMed: 24413735] [Full Text: https://doi.org/10.1038/ng.2874]
Roman, C. A. J., Baltimore, D. Genetic evidence that the RAG1 protein directly participates in V(D)J recombination through substrate recognition. Proc. Nat. Acad. Sci. 93: 2333-2338, 1996. [PubMed: 8637873] [Full Text: https://doi.org/10.1073/pnas.93.6.2333]
Santagata, S., Gomez, C. A., Sobacchi, C., Bozzi, F., Abinun, M., Pasic, S., Cortes, P., Vezzoni, P., Villa, A. N-terminal RAG1 frameshift mutations in Omenn's syndrome: internal methionine usage leads to partial V(D)J recombination activity and reveals a fundamental role in vivo for the N-terminal domains. Proc. Nat. Acad. Sci. 97: 14572-14577, 2000. [PubMed: 11121059] [Full Text: https://doi.org/10.1073/pnas.97.26.14572]
Schatz, D. G., Oettinger, M. A., Baltimore, D. The V(D)J recombination activating gene, RAG-1. Cell 59: 1035-1048, 1989. [PubMed: 2598259] [Full Text: https://doi.org/10.1016/0092-8674(89)90760-5]
Schuetz, C., Huck, K., Gudowius, S., Megahed, M., Feyen, O., Hubner, B., Schneider, D. T., Manfras, B., Pannicke, U., Willemze, R., Knuchel, R., Gobel, U., Schulz, A., Borkhardt, A., Friedrich, W., Schwarz, K., Niehues, T. An immunodeficiency disease with RAG mutations and granulomas. New Eng. J. Med. 358: 2030-2038, 2008. [PubMed: 18463379] [Full Text: https://doi.org/10.1056/NEJMoa073966]
Schwarz, K., Gauss, G. H., Ludwig, L., Pannicke, U., Li, Z., Linder, D., Friedrich, W., Seger, R. A., Hansen-Hagge, T. E., Desiderio, S., Lieber, M. R., Bartram, C. R. RAG mutations in human B cell-negative SCID. Science 274: 97-99, 1996. [PubMed: 8810255] [Full Text: https://doi.org/10.1126/science.274.5284.97]
Sherrington, P. D., Forster, A., Seawright, A., van Heyningen, V., Rabbitts, T. H. Human RAG2, like RAG1, is on chromosome 11 band p13 and therefore not linked to ataxia telangiectasia complementation groups. Genes Chromosomes Cancer 5: 404-406, 1992. [PubMed: 1283330] [Full Text: https://doi.org/10.1002/gcc.2870050417]
Simkus, C., Anand, P., Bhattacharyya, A., Jones, J. M. Biochemical and folding defects in a RAG1 variant associated with Omenn syndrome. J. Immun. 179: 8332-8340, 2007. [PubMed: 18056378] [Full Text: https://doi.org/10.4049/jimmunol.179.12.8332]
Tabori, U., Mark, Z., Amariglio, N., Etzioni, A., Golan, H., Biloray, B., Toren, A., Rechavi, G., Dalal, I. Detection of RAG mutations and prenatal diagnosis in families presenting with either T-B- severe combined immunodeficiency or Omenn's syndrome. Clin. Genet. 65: 322-326, 2004. [PubMed: 15025726] [Full Text: https://doi.org/10.1111/j.1399-0004.2004.00227.x]
Villa, A., Santagata, S., Bozzi, F., Giliani, S., Frattini, A., Imberti, L., Gatta, L. B., Ochs, H. D., Schwarz, K., Notarangelo, L. D., Vezzoni, P., Spanopoulou, E. Partial V(D)J recombination activity leads to Omenn syndrome. Cell 93: 885-896, 1998. [PubMed: 9630231] [Full Text: https://doi.org/10.1016/s0092-8674(00)81448-8]
Villa, A., Sobacchi, C., Notarangelo, L. D., Bozzi, F., Abinun, M., Abrahamsen, T. G., Arkwright, P. D., Baniyash, M., Brooks, E. G., Conley, M. E., Cortes, P., Duse, M., and 21 others. V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. Blood 97: 81-88, 2001. [PubMed: 11133745] [Full Text: https://doi.org/10.1182/blood.v97.1.81]
Wienholds, E., Schulte-Merker, S., Walderich, B., Plasterk, R. H. A. Target-selected inactivation of the zebrafish rag1 gene. Science 297: 99-102, 2002. [PubMed: 12098699] [Full Text: https://doi.org/10.1126/science.1071762]
Xiao, Z., Yannone, S. M., Dunn, E., Cowan, M. J. A novel missense RAG-1 mutation results in T-B-NK+ SCID in Athabascan-speaking Dine Indians from the Canadian Northwest Territories. Europ. J. Hum. Genet. 17: 205-212, 2009. [PubMed: 18701881] [Full Text: https://doi.org/10.1038/ejhg.2008.150]
Yarnell Schultz, H. Y., Landree, M. A., Qiu, J., Kale, S. B., Roth, D. B. Joining-deficient RAG1 mutants block V(D)J recombination in vivo and hairpin opening in vitro. Molec. Cell 7: 65-75, 2001. [PubMed: 11172712] [Full Text: https://doi.org/10.1016/s1097-2765(01)00155-1]
Yu, W., Misulovin, Z., Suh, H., Hardy, R. R., Jankovic, M., Yannoutsos, N., Nussenzweig, M. C. Coordinate regulation of RAG1 and RAG2 by cell type-specific DNA elements 5-prime of RAG2. Science 285: 1080-1084, 1999. [PubMed: 10446057] [Full Text: https://doi.org/10.1126/science.285.5430.1080]
Yu, X., Almeida, J., Darko, S., van der Burg, M., DeRavin, S. S., Malech, H., Gennery, A., Chinn, I., Markert, M. L., Douek, D. C., Milner, J. D. Human syndromes of immunodeficiency and dysregulation are characterized by distinct defects in T-cell receptor repertoire development. J. Allergy Clin. Immun. 133: 1109-1115, 2014. [PubMed: 24406074] [Full Text: https://doi.org/10.1016/j.jaci.2013.11.018]