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Gene

DEF6

DEF6 guanine nucleotide exchange factor

Summary

Cytogenetic location
6p21.31
Coordinates
Chromosome 6: 35,297,818–35,321,771 (GRCh38)
Exons
11 exons across 24 kb
Protein
631 amino acids
Inheritance
Autosomal recessive
Also known as
IBP, SLAT, SWAP70L
MANE Select transcript
ENST00000316637.7NM_022047.4
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

  • IPEX Syndrome and Other Tregopathies

    • DEF6 deficiency (immunodeficiency 87)Autosomal recessive

      Autoimmunity, enteropathy and infections caused by changes in both copies of DEF6, which reduces CTLA4 availability.

      • ClinGen rates the link moderate
      • 2 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 moderate
      • 2 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 DEF6 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 6, with a bracket where DEF6 sits. DEF6 and 17 genes near it on chromosome 6, from 34,809,795 to 35,809,794.Chromosome 66p21.31p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12q13q14.1q14.2q14.3q15q16.1q16.2q16.3q21q22.1q22.2q22.31q22.32q22.33q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q26q2735 Mb35.2 Mb35.4 Mb35.6 Mb35.8 MbBLTP3A: 34,792,024–34,885,350, forward strandBLTP3ATAF11: 34,829,083–34,889,192, reverse strandTAF11ANKS1A: 34,889,243–35,091,421, forward strandANKS1ATCP11: 35,118,071–35,148,610, reverse strandTCP11SCUBE3: 35,213,859–35,253,080, forward strandSCUBE3ZNF76: 35,258,909–35,295,985, forward strandZNF76DEF6: 35,297,818–35,321,771, forward strandDEF6PPARD: 35,342,530–35,428,193, forward strandPPARDFANCE: 35,452,315–35,467,106, forward strandFANCERPL10A: 35,468,366–35,470,786, forward strandRPL10ATEAD3: 35,473,597–35,497,868, reverse strandTEAD3TULP1: 35,497,874–35,512,941, reverse strandTULP1FKBP5: 35,572,945–35,728,622, reverse strandFKBP5ARMC12: 35,737,028–35,749,079, forward strandARMC12CLPSL2: 35,776,535–35,779,557, forward strandCLPSL2CLPSL1: 35,781,019–35,793,675, forward strandCLPSL1CLPS: 35,794,982–35,798,251, reverse strandCLPSLHFPL5: 35,797,206–35,845,397, forward strandLHFPL5Diagram of DEF6: 11 exons on the forward strand of chromosome 6Exon 4: 1 known disease-causing siteExon 1: 35,297,818–35,297,952, 135 basesExon 2: 35,309,670–35,309,810, 141 basesExon 3: 35,310,459–35,310,644, 186 basesExon 4: 35,312,302–35,312,538, 237 basesExon 5: 35,312,626–35,312,772, 147 basesExon 6: 35,317,891–35,317,999, 109 basesExon 7: 35,318,173–35,318,471, 299 basesExon 8: 35,319,524–35,319,690, 167 basesExon 9: 35,319,819–35,320,017, 199 basesExon 10: 35,320,884–35,320,974, 91 basesExon 11: 35,321,187–35,321,771, 585 bases1115′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 2.3 kb of the gene's 24 kb; 1,896 of those bases code for the protein.

How a genome test reads DEF6

1

position in DEF6 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 24 kb of DEF6, introns included, not only the 2.3 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.). DEF6 gene: DEF6 guanine nucleotide exchange factor. Retrieved 16 October 2026, from https://dantelabs.com/genes/def6

Vancouver

Dante Labs. DEF6 gene: DEF6 guanine nucleotide exchange factor [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/def6

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