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Gene

RAG1

recombination activating 1

Summary

Cytogenetic location
11p12
Coordinates
Chromosome 11: 36,568,007–36,579,762 (GRCh38)
Exons
2 exons across 11.8 kb
Protein
1,043 amino acids
Inheritance
Autosomal recessive
Also known as
RNF74, MGC43321
MANE Select transcript
ENST00000299440.6NM_000448.3
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • Severe Combined Immunodeficiency

    • Autosomal recessive

      Severe combined immunodeficiency (SCID) comprises a group of rare monogenic primary immunodeficiency disorders characterized by a lack of functional peripheral T lymphocytes resulting in early-onset severe respiratory infections and failure to thrive. They are classified according to immunological phenotype into SCID with absence of T cells but presence of B cells (T-B+ SCID) or SCID with absence of both (T-B- SCID). Both of these groups include several forms, with or without natural killer (NK) cells.

      • ClinGen rates the link definitive
      • 6 GenCC submitters rate it definitive or strong

Broader groupings

  • Other Inborn Errors of Immunity

    • Immunodeficiency Disease

      One of 170 genes linked to it

      Disease in which there is a deficiency or defect in the mechanisms of immunity, either cellular or humoral.

      • ClinGen rates the link definitive
      • 6 GenCC submitters rate it definitive or strong
      What knowing changes

      HSCT for SCID and severe PIDs; immunoglobulin replacement (IVIG/SCIG) for antibody deficiencies; leniolisib (Joenja, FDA 2023) for APDS; gene therapy for ADA-SCID; abatacept for CTLA4/LRBA deficiency; prophylactic antibiotics; G-CSF for CGD

Inheritance

Autosomal recessive
It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.

How RAG1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 11, with a bracket where RAG1 sits. RAG1 and 6 genes near it on chromosome 11, from 36,073,885 to 37,073,884.Chromosome 1111p12p15.5p15.4p15.3p15.2p15.1p14.3p14.2p14.1p13p12p11.2p11.12p11.11q11q12.1q12.2q12.3q13.1q13.2q13.3q13.4q13.5q14.1q14.2q14.3q21q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q2536.2 Mb36.4 Mb36.6 Mb36.8 Mb37 MbLDLRAD3: 35,943,981–36,274,286, forward strandLDLRAD3COMMD9: 36,269,284–36,289,449, reverse strandCOMMD9PRR5L: 36,296,120–36,465,209, forward strandPRR5LTRAF6: 36,483,769–36,510,308, reverse strandTRAF6RAG1: 36,568,007–36,579,762, forward strandRAG1RAG2: 36,575,574–36,598,279, reverse strandRAG2IFTAP: 36,594,369–36,675,695, forward strandIFTAPDiagram of RAG1: 2 exons on the forward strand of chromosome 11Exon 2: 144 known disease-causing sitesExon 1: 36,568,007–36,568,122, 116 basesExon 2: 36,573,291–36,579,762, 6,472 bases125′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 6.6 kb of the gene's 11.8 kb; 3,132 of those bases code for the protein.

How a genome test reads RAG1

144

positions in RAG1 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 11.8 kb of RAG1, introns included, not only the 6.6 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). RAG1 gene: recombination activating 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/rag1

Vancouver

Dante Labs. RAG1 gene: recombination activating 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/rag1

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