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Gene

ZIC3

Zic family zinc finger 3

Summary

Cytogenetic location
Xq26.3
Coordinates
Chromosome X: 137,566,127–137,572,102 (GRCh38)
Exons
3 exons across 6 kb
Protein
467 amino acids
Also known as
HTX, ZNF203
Previous symbols
HTX1
MANE Select transcript
ENST00000287538.10NM_003413.4
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

  • Heterotaxy & Laterality Defects

    • Congenital Heart Disease with Heterotaxy

      Heart defects present at birth that occur together with variable left-right patterning defects of other organs.

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

      Abnormal left-right arrangement of the internal organs, caused by changes in genes such as ZIC3 (X-linked), NODAL, CFC1, MMP21 and PKD1L1, often with complex heart defects and spleen abnormalities.

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

      Knowing about it supports heart and abdominal imaging, infection precautions if the spleen is absent, and reproductive counselling.

How ZIC3 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome X, with a bracket where ZIC3 sits. ZIC3 and 0 genes near it on chromosome X, from 137,069,115 to 138,069,114.Chromosome XXq26.3p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q28137.2 Mb137.4 Mb137.6 Mb137.8 Mb138 MbZIC3: 137,566,127–137,572,102, forward strandZIC3Diagram of ZIC3: 3 exons on the forward strand of chromosome XExon 1: 20 known disease-causing sitesExon 2: 3 known disease-causing sitesExon 1: 137,566,127–137,567,751, 1,625 basesExon 2: 137,568,902–137,569,065, 164 basesExon 3: 137,569,891–137,572,102, 2,212 bases1235′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 6 kb; 1,404 of those bases code for the protein.

How a genome test reads ZIC3

24

positions in ZIC3 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 6 kb of ZIC3, 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.). ZIC3 gene: Zic family zinc finger 3. Retrieved 17 October 2026, from https://dantelabs.com/genes/zic3

Vancouver

Dante Labs. ZIC3 gene: Zic family zinc finger 3 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/zic3

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