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Gene

LAT

linker for activation of T cells

Summary

Cytogenetic location
16p11.2
Coordinates
Chromosome 16: 28,985,052–28,990,784 (GRCh38)
Exons
12 exons across 5.7 kb
Protein
233 amino acids
Inheritance
Autosomal recessive
Also known as
LAT1
MANE Select transcript
ENST00000395456.7NM_001014987.2
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 LAT is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
Chromosome 16, with a bracket where LAT sits. LAT and 25 genes near it on chromosome 16, from 28,487,918 to 29,487,917.Chromosome 1616p11.2p13.3p13.2p13.13p13.12p13.11p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q13q21q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.328.6 Mb28.8 Mb29 Mb29.2 Mb29.4 Mb: 28,456,371–28,492,098, reverse strandCLN3: 28,474,111–28,495,575, reverse strandCLN3APOBR: 28,494,635–28,498,964, forward strandAPOBRIL27: 28,499,360–28,512,051, reverse strandIL27NUPR1: 28,532,708–28,539,068, reverse strandNUPR1SGF29: 28,538,176–28,591,792, forward strandSGF29SULT1A2: 28,589,688–28,599,913, reverse strandSULT1A2SULT1A1: 28,604,997–28,612,503, reverse strandSULT1A1NPIPB8: 28,637,654–28,658,744, forward strandNPIPB8EIF3C: 28,688,558–28,745,938, forward strandEIF3CNPIPB9: 28,751,787–28,772,864, forward strandNPIPB9ATXN2L: 28,822,983–28,837,237, forward strandATXN2LTUFM: 28,841,618–28,846,419, reverse strandTUFMSH2B1: 28,846,584–28,875,103, forward strandSH2B1ATP2A1: 28,878,383–28,904,511, forward strandATP2A1RABEP2: 28,898,740–28,936,526, reverse strandRABEP2CD19: 28,931,965–28,939,342, forward strandCD19NFATC2IP: 28,950,807–28,967,092, forward strandNFATC2IPSPNS1: 28,974,126–28,984,548, forward strandSPNS1LAT: 28,985,052–28,990,784, forward strandLATNPIPB11: 29,381,310–29,406,711, reverse strandNPIPB11BOLA2-SMG1P6: 29,443,230–29,454,651, reverse strandBOLA2-SMG1P6BOLA2: 29,453,587–29,455,012, reverse strandBOLA2SLX1B: 29,454,501–29,458,223, forward strandSLX1BSULT1A4: 29,458,993–29,464,979, forward strandSULT1A4NPIPB12: 29,483,534–29,508,595, reverse strandDiagram of LAT: 12 exons on the forward strand of chromosome 16Exon 1: 28,985,052–28,985,517, 466 basesExon 2: 28,985,713–28,985,740, 28 basesExon 3: 28,985,854–28,985,888, 35 basesExon 4: 28,986,135–28,986,216, 82 basesExon 5: 28,986,382–28,986,446, 65 basesExon 6: 28,986,540–28,986,569, 30 basesExon 7: 28,986,657–28,986,714, 58 basesExon 8: 28,986,799–28,986,893, 95 basesExon 9: 28,989,527–28,989,589, 63 basesExon 10: 28,989,774–28,989,839, 66 basesExon 11: 28,989,933–28,990,019, 87 basesExon 12: 28,990,189–28,990,784, 596 bases1234567891011125′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 1.7 kb of the gene's 5.7 kb; 702 of those bases code for the protein.

How a genome test reads LAT

1

position in LAT 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 5.7 kb of LAT, introns included, not only the 1.7 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.). LAT gene: linker for activation of T cells. Retrieved 16 October 2026, from https://dantelabs.com/genes/lat

Vancouver

Dante Labs. LAT gene: linker for activation of T cells [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/lat

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