Skip to content
Use your HSA or FSA funds

Gene

NRXN1

neurexin 1

Summary

Cytogenetic location
2p16.3
Coordinates
Chromosome 2: 49,918,503–51,032,132 (GRCh38)
Exons
23 exons across 1,113.6 kb
Protein
1,507 amino acids
Also known as
KIAA0578, Hs.22998
MANE Select transcript
ENST00000401669.7NM_001330078.2
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 report relevant to this gene

  • Schizophrenia Panel

    • Schizophrenia

      A major psychotic disorder characterized by abnormalities in the perception or expression of reality. It affects the cognitive and psychomotor functions. Common clinical signs and symptoms include delusions, hallucinations, disorganized thinking, and retreat from reality.

      • 1 GenCC submitter rates it definitive or strong

How NRXN1 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 NRXN1 sits. NRXN1 and 1 gene near it on chromosome 2, from 48,804,873 to 52,145,762.Chromosome 22p16.3p25.3p25.2p25.1p24.3p24.2p24.1p23.3p23.2p23.1p22.3p22.2p22.1p21p16.3p16.2p16.1p15p14p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13q14.1q14.2q14.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q34q35q36.1q36.2q36.3q37.1q37.2q37.349 Mb49.5 Mb50 Mb50.5 Mb51 Mb51.5 Mb52 MbFSHR: 48,962,157–49,154,527, reverse strandFSHRNRXN1: 49,918,503–51,032,132, reverse strandNRXN1Diagram of NRXN1: 23 exons on the reverse strand of chromosome 2Exon 21: 3 known disease-causing sitesExon 20: 3 known disease-causing sitesExon 19: 1 known disease-causing siteExon 18: 5 known disease-causing sitesExon 16: 1 known disease-causing siteExon 15: 1 known disease-causing siteExon 14: 2 known disease-causing sitesExon 13: 3 known disease-causing sitesExon 11: 3 known disease-causing sitesExon 10: 3 known disease-causing sitesExon 9: 1 known disease-causing siteExon 8: 2 known disease-causing sitesExon 5: 2 known disease-causing sitesExon 4: 1 known disease-causing siteExon 2: 7 known disease-causing sitesExon 23: 49,918,503–49,922,251, 3,749 basesExon 22: 49,943,704–49,943,791, 88 basesExon 21: 50,053,271–50,053,590, 320 basesExon 20: 50,054,955–50,055,044, 90 basesExon 19: 50,091,323–50,091,494, 172 basesExon 18: 50,236,789–50,236,970, 182 basesExon 17: 50,465,442–50,465,561, 120 basesExon 16: 50,472,298–50,472,471, 174 basesExon 15: 50,495,905–50,496,095, 191 basesExon 14: 50,497,333–50,497,714, 382 basesExon 13: 50,506,495–50,506,617, 123 basesExon 12: 50,528,625–50,528,651, 27 basesExon 11: 50,531,227–50,531,430, 204 basesExon 10: 50,538,253–50,538,636, 384 basesExon 9: 50,552,587–50,553,025, 439 basesExon 8: 50,620,022–50,620,183, 162 basesExon 7: 50,621,226–50,621,249, 24 basesExon 6: 50,623,314–50,623,615, 302 basesExon 5: 50,921,869–50,921,880, 12 basesExon 4: 50,922,658–50,922,687, 30 basesExon 3: 50,925,938–50,925,955, 18 basesExon 2: 51,027,502–51,029,194, 1,693 basesExon 1: 51,031,981–51,032,132, 152 bases23201510515′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 9 kb of the gene's 1,113.6 kb; 4,524 of those bases code for the protein.

How a genome test reads NRXN1

54

positions in NRXN1 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 1,113.6 kb of NRXN1, introns included, not only the 9 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.). NRXN1 gene: neurexin 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/nrxn1

Vancouver

Dante Labs. NRXN1 gene: neurexin 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/nrxn1

One test. A lifetime of answers.

From $449Free shipping · Results in 6–8 weeks

Get my Genome Test