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Gene

NLGN3

neuroligin 3

Summary

Cytogenetic location
Xq13.1
Coordinates
Chromosome X: 71,144,841–71,171,201 (GRCh38)
Exons
8 exons across 26.4 kb
Protein
848 amino acids
Also known as
HNL3, KIAA1480, ASPGX1, AUTSX1
MANE Select transcript
ENST00000358741.4NM_181303.2
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

  • Autism Spectrum Disorder

    • Autism, susceptibility to (single-gene forms)

      Single-gene contributions to autism, including variants in NLGN3, NLGN4X, PTCHD1, SHANK2, TBR1 and CHD8.

      • 1 GenCC submitter rates it definitive or strong

  • Epilepsy (Full Panel)

    • X-Linked Complex Neurodevelopmental Disorder

      A complex neurodevelopmental disorder that is transmitted via X-linked inheritance, and is characterized by intellectual disability, autism and epilepsy.

      • ClinGen rates the link moderate
      • 1 GenCC submitter rates it definitive or strong

How NLGN3 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome X, with a bracket where NLGN3 sits. NLGN3 and 16 genes near it on chromosome X, from 70,658,021 to 71,658,020.Chromosome XXq13.1p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q2870.8 Mb71 Mb71.2 Mb71.4 Mb71.6 MbTEX11: 70,528,940–70,908,711, reverse strandTEX11SLC7A3: 70,925,556–70,931,149, reverse strandSLC7A3SNX12: 70,963,111–71,073,426, reverse strandSNX12FOXO4: 71,095,839–71,103,535, forward strandCXorf65: 71,103,889–71,106,788, reverse strandCXorf65: 71,103,987–71,111,575, reverse strandIL2RG: 71,107,404–71,112,108, reverse strandIL2RGMED12: 71,118,543–71,144,103, forward strandMED12NLGN3: 71,144,841–71,171,201, forward strandNLGN3GJB1: 71,212,811–71,225,519, forward strandGJB1ZMYM3: 71,239,617–71,255,269, reverse strandZMYM3NONO: 71,254,270–71,301,522, forward strandNONOITGB1BP2: 71,301,717–71,305,371, forward strandITGB1BP2TAF1: 71,366,129–71,532,374, forward strandTAF1OGT: 71,533,068–71,575,892, forward strandOGTGCNA: 71,578,436–71,613,590, forward strandGCNACXCR3: 71,615,912–71,618,545, reverse strandCXCR3Diagram of NLGN3: 8 exons on the forward strand of chromosome XExon 2: 1 known disease-causing siteExon 5: 1 known disease-causing siteExon 8: 1 known disease-causing siteExon 1: 71,144,841–71,144,964, 124 basesExon 2: 71,147,550–71,148,206, 657 basesExon 3: 71,148,846–71,148,905, 60 basesExon 4: 71,153,477–71,153,536, 60 basesExon 5: 71,155,214–71,155,363, 150 basesExon 6: 71,164,143–71,164,328, 186 basesExon 7: 71,167,011–71,167,800, 790 basesExon 8: 71,169,254–71,171,201, 1,948 bases123456785′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 4 kb of the gene's 26.4 kb; 2,547 of those bases code for the protein.

How a genome test reads NLGN3

3

positions in NLGN3 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 26.4 kb of NLGN3, introns included, not only the 4 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.). NLGN3 gene: neuroligin 3. Retrieved 17 October 2026, from https://dantelabs.com/genes/nlgn3

Vancouver

Dante Labs. NLGN3 gene: neuroligin 3 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/nlgn3

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