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Gene

NLGN4X

neuroligin 4 X-linked

Summary

Cytogenetic location
Xp22.32-p22.31
Coordinates
Chromosome X: 5,890,042–6,228,867 (GRCh38)
Exons
6 exons across 338.8 kb
Protein
816 amino acids
Also known as
KIAA1260, NLGN, HLNX
Previous symbols
NLGN4
MANE Select transcript
ENST00000381095.8NM_181332.3
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

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.

      • 4 GenCC submitters rate 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 definitive
      • 1 GenCC submitter rates it definitive or strong

How NLGN4X 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 NLGN4X sits. NLGN4X and 1 gene near it on chromosome X, from 5,551,216 to 6,567,693.Chromosome XXp22.32-p22.31p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q285.6 Mb5.8 Mb6 Mb6.2 Mb6.4 MbNLGN4X: 5,890,042–6,228,867, reverse strandNLGN4XVCX3A: 6,533,618–6,535,118, reverse strandVCX3ADiagram of NLGN4X: 6 exons on the reverse strand of chromosome XExon 4: 1 known disease-causing siteExon 6: 5,890,042–5,893,666, 3,625 basesExon 5: 5,903,077–5,903,866, 790 basesExon 4: 5,909,054–5,909,239, 186 basesExon 3: 6,029,280–6,029,432, 153 basesExon 2: 6,150,995–6,151,771, 777 basesExon 1: 6,228,541–6,228,867, 327 bases6543215′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 5.9 kb of the gene's 338.8 kb; 2,451 of those bases code for the protein.

How a genome test reads NLGN4X

2

positions in NLGN4X 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 338.8 kb of NLGN4X, introns included, not only the 5.9 kb of exons.

Genes linked to the same conditions

Traits linked to NLGN4X

The Human Phenotype Ontology lists these as features of the rare conditions NLGN4X can cause. Each trait's page lists the other genes linked to it.

External links

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.). NLGN4X gene: neuroligin 4 X-linked. Retrieved 17 October 2026, from https://dantelabs.com/genes/nlgn4x

Vancouver

Dante Labs. NLGN4X gene: neuroligin 4 X-linked [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/nlgn4x

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