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Gene

NHEJ1

non-homologous end joining factor 1

Summary

Cytogenetic location
2q35
Coordinates
Chromosome 2: 219,069,357–219,160,815 (GRCh38)
Exons
8 exons across 91.5 kb
Protein
299 amino acids
Inheritance
Autosomal recessive
Also known as
Cernunnos, XLF, FLJ12610
MANE Select transcript
ENST00000356853.10NM_024782.3
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
      • 3 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
      • 3 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 NHEJ1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 2, with a bracket where NHEJ1 sits. NHEJ1 and 43 genes near it on chromosome 2, from 218,615,086 to 219,615,085.Chromosome 22q35p25.3p25.2p25.1p24.3p24.2p24.1p23.3p23.2p23.1p22.3p22.2p22.1p21p16.3p16.2p16.1p15p14p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13q14.1q14.2q14.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q34q35q36.1q36.2q36.3q37.1q37.2q37.3218.8 Mb219 Mb219.2 Mb219.4 Mb219.6 MbPLCD4: 218,607,855–218,637,186, forward strandPLCD4ZNF142: 218,633,329–218,659,655, reverse strandZNF142BCS1L: 218,658,764–218,668,759, forward strandBCS1LRNF25: 218,662,081–218,672,009, reverse strandRNF25STK36: 218,672,027–218,702,717, forward strandSTK36TTLL4: 218,710,773–218,759,724, forward strandTTLL4CYP27A1: 218,781,688–218,825,335, forward strandCYP27A1PRKAG3: 218,819,050–218,832,086, reverse strandPRKAG3WNT6: 218,859,795–218,874,233, forward strandWNT6WNT10A: 218,880,852–218,899,581, forward strandWNT10ACDK5R2: 218,959,666–218,962,155, forward strandCDK5R2FEV: 218,981,087–218,985,566, reverse strandFEVCRYBA2: 218,990,189–218,994,270, reverse strandCRYBA2CFAP65: 219,002,846–219,041,527, reverse strandCFAP65IHH: 219,054,424–219,061,064, reverse strandIHHNHEJ1: 219,069,357–219,160,815, reverse strandNHEJ1: 219,075,329–219,170,827, reverse strandSLC23A3: 219,161,465–219,170,095, reverse strandSLC23A3CNPPD1: 219,170,704–219,182,664, reverse strandCNPPD1RETREG2: 219,176,225–219,185,917, forward strandZFAND2B: 219,195,237–219,209,651, forward strandABCB6: 219,209,765–219,219,012, reverse strandABCB6: 219,209,772–219,222,738, reverse strandATG9A: 219,219,380–219,230,383, reverse strandANKZF1: 219,229,769–219,236,679, forward strandGLB1L: 219,236,598–219,245,478, reverse strandGLB1LSTK16: 219,245,212–219,250,339, forward strandTUBA4A: 219,249,710–219,277,902, reverse strandTUBA4B: 219,253,243–219,272,197, forward strandDNAJB2: 219,279,308–219,286,900, forward strandDNAJB2PTPRN: 219,289,623–219,309,648, reverse strandPTPRNRESP18: 219,327,407–219,335,552, reverse strandRESP18DNPEP: 219,360,090–219,400,022, reverse strandDNPEPDES: 219,417,474–219,426,740, forward strandDESSPEG: 219,434,471–219,493,629, forward strandSPEG: 219,491,867–219,498,244, forward strandSPEGNB: 219,496,129–219,498,287, forward strandSPEGNBGMPPA: 219,498,618–219,513,898, forward strandGMPPAASIC4: 219,514,170–219,538,772, forward strandASIC4CHPF: 219,538,949–219,543,818, reverse strandCHPFTMEM198: 219,543,130–219,550,595, forward strandOBSL1: 219,550,727–219,572,076, reverse strandOBSL1INHA: 219,569,162–219,575,711, forward strandSTK11IP: 219,595,805–219,616,452, forward strandSTK11IPDiagram of NHEJ1: 8 exons on the reverse strand of chromosome 2Exon 6: 2 known disease-causing sitesExon 5: 3 known disease-causing sitesExon 4: 3 known disease-causing sitesExon 3: 2 known disease-causing sitesExon 2: 8 known disease-causing sitesExon 8: 219,069,357–219,076,455, 7,099 basesExon 7: 219,077,246–219,077,364, 119 basesExon 6: 219,078,089–219,078,206, 118 basesExon 5: 219,146,680–219,146,738, 59 basesExon 4: 219,147,657–219,147,795, 139 basesExon 3: 219,157,472–219,157,684, 213 basesExon 2: 219,158,186–219,158,362, 177 basesExon 1: 219,160,720–219,160,815, 96 bases864215′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 8 kb of the gene's 91.5 kb; 900 of those bases code for the protein.

How a genome test reads NHEJ1

26

positions in NHEJ1 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 91.5 kb of NHEJ1, introns included, not only the 8 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.). NHEJ1 gene: non-homologous end joining factor 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/nhej1

Vancouver

Dante Labs. NHEJ1 gene: non-homologous end joining factor 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/nhej1

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