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Gene

VSX2

visual system homeobox 2

Summary

Cytogenetic location
14q24.3
Coordinates
Chromosome 14: 74,239,449–74,262,738 (GRCh38)
Exons
5 exons across 23.3 kb
Protein
361 amino acids
Also known as
RET1
Previous symbols
HOX10, CHX10
MANE Select transcript
ENST00000261980.3NM_182894.3
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

  • Microphthalmia, Anophthalmia & Coloboma

    • Isolated Anophthalmia, Microphthalmia & Coloboma

      Eye malformations without other features, including nanophthalmos, caused by changes in genes such as VSX2, RAX, MFRP, PRSS56 and others.

      • 4 GenCC submitters rate it definitive or strong
      What knowing changes

      People with nanophthalmos (often MFRP or PRSS56) have a raised risk of angle-closure glaucoma and need regular eye checks; a genetic diagnosis also informs recurrence risk.

How VSX2 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 14, with a bracket where VSX2 sits. VSX2 and 18 genes near it on chromosome 14, from 73,751,094 to 74,751,093.Chromosome 1414q24.3p13p12p11.2p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.11q32.12q32.13q32.2q32.31q32.32q32.3373.8 Mb74 Mb74.2 Mb74.4 Mb74.6 MbMIDEAS: 73,715,122–73,790,285, reverse strandMIDEASPTGR2: 73,851,792–73,885,726, forward strandPTGR2: 73,851,971–73,932,278, forward strandZNF410: 73,886,201–73,932,521, forward strandZNF410FAM161B: 73,931,501–73,950,414, reverse strandFAM161BCOQ6: 73,949,926–73,963,670, forward strandCOQ6ENTPD5: 73,956,688–74,019,399, reverse strandENTPD5BBOF1: 74,019,341–74,082,863, forward strandBBOF1ALDH6A1: 74,055,997–74,084,492, reverse strandALDH6A1LIN52: 74,084,943–74,201,493, forward strandLIN52VSX2: 74,239,449–74,262,738, forward strandVSX2ABCD4: 74,285,269–74,303,068, reverse strandABCD4VRTN: 74,303,069–74,360,011, forward strandVRTNSYNDIG1L: 74,405,894–74,426,325, reverse strandSYNDIG1LNPC2: 74,427,119–74,494,177, reverse strandNPC2ISCA2: 74,493,721–74,499,758, forward strandISCA2LTBP2: 74,498,163–74,612,378, reverse strandLTBP2AREL1: 74,653,437–74,713,117, reverse strandAREL1FCF1: 74,713,144–74,750,706, forward strandFCF1Diagram of VSX2: 5 exons on the forward strand of chromosome 14Exon 1: 36 known disease-causing sitesExon 2: 3 known disease-causing sitesExon 3: 1 known disease-causing siteExon 4: 10 known disease-causing sitesExon 5: 4 known disease-causing sitesExon 1: 74,239,449–74,239,931, 483 basesExon 2: 74,241,182–74,241,266, 85 basesExon 3: 74,245,165–74,245,288, 124 basesExon 4: 74,259,602–74,259,782, 181 basesExon 5: 74,260,594–74,262,738, 2,145 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 3 kb of the gene's 23.3 kb; 1,086 of those bases code for the protein.

How a genome test reads VSX2

60

positions in VSX2 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 23.3 kb of VSX2, introns included, not only the 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.
  • 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.). VSX2 gene: visual system homeobox 2. Retrieved 16 October 2026, from https://dantelabs.com/genes/vsx2

Vancouver

Dante Labs. VSX2 gene: visual system homeobox 2 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/vsx2

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