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Gene

PAX1

paired box 1

Summary

Cytogenetic location
20p11.22
Coordinates
Chromosome 20: 21,705,664–21,718,481 (GRCh38)
Exons
5 exons across 12.8 kb
Protein
457 amino acids
MANE Select transcript
ENST00000613128.5NM_001257096.2
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

No Genome Test report reads PAX1 yet. The test sequences your whole genome, so your data includes it all the same.

How PAX1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 20, with a bracket where PAX1 sits. PAX1 and 4 genes near it on chromosome 20, from 21,212,073 to 22,212,072.Chromosome 2020p11.22p13p12.3p12.2p12.1p11.23p11.22p11.21p11.1q11.1q11.21q11.22q11.23q12q13.11q13.12q13.13q13.2q13.31q13.32q13.3321.4 Mb21.6 Mb21.8 Mb22 Mb22.2 MbKIZ: 21,125,975–21,273,506, forward strandKIZXRN2: 21,303,281–21,390,251, forward strandXRN2NKX2-4: 21,395,152–21,397,526, reverse strandNKX2-4NKX2-2: 21,511,017–21,514,070, reverse strandNKX2-2PAX1: 21,705,664–21,718,481, forward strandPAX1Diagram of PAX1: 5 exons on the forward strand of chromosome 20Exon 2: 3 known disease-causing sitesExon 4: 2 known disease-causing sitesExon 1: 21,705,664–21,705,998, 335 basesExon 2: 21,706,438–21,707,067, 630 basesExon 3: 21,708,558–21,708,700, 143 basesExon 4: 21,709,222–21,709,444, 223 basesExon 5: 21,714,471–21,718,481, 4,011 bases123455′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 5.3 kb of the gene's 12.8 kb; 1,374 of those bases code for the protein.

How a genome test reads PAX1

5

positions in PAX1 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 12.8 kb of PAX1, introns included, not only the 5.3 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.
  • 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.). PAX1 gene: paired box 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/pax1

Vancouver

Dante Labs. PAX1 gene: paired box 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/pax1

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