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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
ZIC3
Zic family zinc finger 3
Chromosome X Β· Xq26.3
NCBI Gene: 7547Ensembl: ENSG00000156925.13HGNC: HGNC:12874UniProt: O60481
48PubMed Papers
23Diseases
0Drugs
41Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
RNA polymerase II cis-regulatory region sequence-specific DNA bindingheart loopingprotein bindingdetermination of liver left/right asymmetryheterotaxy, visceral, 1, X-linkedVACTERL association, X-linked, with or without hydrocephaluscongenital heart defects, multiple types, 1, X-linkedvisceral heterotaxy
✦AI Summary

ZIC3 is an X-linked C2H2 zinc finger transcription factor essential for early vertebrate development, functioning primarily as a transcriptional activator that binds to the GLI-consensus sequence 5'-GGGTGGTC-3' 1. ZIC3 plays critical roles in establishing the embryonic left-right axis and axial midline development 2. Mechanistically, ZIC3 recruits SWI/SNF chrX remodeling complexes to primed-specific enhancers to maintain and facilitate progression to primed pluripotency 3. Additionally, ZIC3 is involved in early stages of cardiac and neural development, including blood-brain barrier maturation 4. Clinically, ZIC3 mutations cause X-linked heterotaxy syndrome, characterized by disrupted laterality of internal organs and severe congenital heart defects 51. Heterotaxy arises from defects in early left-right axis formation, potentially involving abnormal nodal and ciliary functions 5. ZIC3 mutations have also been associated with additional malformations including lumbosacral and anal anomalies, neural tube defects, and VACTERL-associated hydrocephalus 2. ZIC3 represents one of at least 33 genes implicated in human situs defects 6. Loss of ZIC3 function results in decreased transcriptional activity and aberrant cellular localization, demonstrating the functional impact of pathogenic variants 1.

Sources cited
1
ZIC3 recruits SWI/SNF to chromatin to facilitate and maintain primed pluripotency
PMID: 39358345
2
ZIC3 mutations cause X-linked heterotaxy due to defects in early left-right axis formation
PMID: 29442328
3
Novel ZIC3 mutation (c.890G>T) reduces transcriptional activity and affects GLI-binding site affinity in heterotaxy patients
PMID: 30120289
4
ZIC3 is a zinc finger transcription factor involved in left-right axis establishment and causes laterality defects, congenital heart disease, and neural tube defects when mutated
PMID: 12900569
5
ZIC3 expression correlates with blood-brain barrier differentiation in CNS vascular endothelial cells
PMID: 30188322
6
ZIC3 is among at least 33 genes implicated in human heterotaxy and situs defects
PMID: 38884744
7
ZIC3 controls cardiovascular development and blood-brain barrier maturation; ZIC3 mutations can cause congenital heart anomalies
PMID: 29442325
Disease Associationsβ“˜23
heterotaxy, visceral, 1, X-linkedOpen Targets
0.80Strong
VACTERL association, X-linked, with or without hydrocephalusOpen Targets
0.78Strong
congenital heart defects, multiple types, 1, X-linkedOpen Targets
0.66Moderate
visceral heterotaxyOpen Targets
0.60Moderate
HeterotaxiaOpen Targets
0.56Moderate
congenital heart malformationOpen Targets
0.55Moderate
neurodegenerative diseaseOpen Targets
0.51Moderate
anorectal malformationOpen Targets
0.37Weak
genetic disorderOpen Targets
0.34Weak
Alzheimer diseaseOpen Targets
0.28Weak
lysosomal storage diseaseOpen Targets
0.28Weak
multiple sclerosisOpen Targets
0.28Weak
Parkinson diseaseOpen Targets
0.28Weak
facial morphologyOpen Targets
0.19Weak
Abnormality of refractionOpen Targets
0.18Weak
Mobius syndromeOpen Targets
0.07Suggestive
heterotaxy, visceral, 12, autosomalOpen Targets
0.06Suggestive
3M syndromeOpen Targets
0.05Suggestive
spondylocostal dysostosis 4, autosomal recessiveOpen Targets
0.05Suggestive
X-linked intellectual disability with marfanoid habitusOpen Targets
0.05Suggestive
Congenital heart defects, multiple types, 1, X-linkedUniProt
Heterotaxy, visceral, 1, X-linkedUniProt
VACTERL association X-linked with or without hydrocephalusUniProt
Pathogenic Variants41
NM_003413.4(ZIC3):c.968C>T (p.Thr323Met)Pathogenic
Heterotaxy, visceral, 1, X-linked
β˜…β˜…β˜†β˜†2022β†’ Residue 323
NM_003413.4(ZIC3):c.1103del (p.Arg368fs)Pathogenic
Heterotaxy, visceral, 1, X-linked|VACTERL association, X-linked, with or without hydrocephalus
β˜…β˜…β˜†β˜†2020β†’ Residue 368
NM_003413.4(ZIC3):c.755C>A (p.Ser252Ter)Pathogenic
Heterotaxy, visceral, 1, X-linked
β˜…β˜†β˜†β˜†2025β†’ Residue 252
NM_003413.4(ZIC3):c.643C>T (p.Gln215Ter)Likely pathogenic
VACTERL association, X-linked, with or without hydrocephalus
β˜…β˜†β˜†β˜†2025β†’ Residue 215
NM_003413.4(ZIC3):c.312C>A (p.Tyr104Ter)Pathogenic
ZIC3-related disorder
β˜…β˜†β˜†β˜†2025β†’ Residue 104
NM_003413.4(ZIC3):c.208C>T (p.Gln70Ter)Pathogenic
Heterotaxy, visceral, 1, X-linked
β˜…β˜†β˜†β˜†2025β†’ Residue 70
NM_003413.4(ZIC3):c.764G>A (p.Trp255Ter)Pathogenic
Heterotaxy, visceral, 1, X-linked
β˜…β˜†β˜†β˜†2024β†’ Residue 255
NM_003413.4(ZIC3):c.97dup (p.Ala33fs)Likely pathogenic
Heterotaxy, visceral, 1, X-linked
β˜…β˜†β˜†β˜†2024β†’ Residue 33
NM_001330661.1(ZIC3):c.1224+3286A>GPathogenic
Heterotaxy, visceral, 1, X-linked
β˜…β˜†β˜†β˜†2024
NM_003413.4(ZIC3):c.1107T>A (p.Phe369Leu)Likely pathogenic
Heterotaxy, visceral, 1, X-linked
β˜…β˜†β˜†β˜†2024β†’ Residue 369
NM_003413.4(ZIC3):c.463G>T (p.Glu155Ter)Pathogenic
Heterotaxy, visceral, 1, X-linked
β˜…β˜†β˜†β˜†2023β†’ Residue 155
NM_003413.4(ZIC3):c.1177_1178del (p.Cys393fs)Likely pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2023β†’ Residue 393
NM_003413.4(ZIC3):c.476_479del (p.Tyr159fs)Pathogenic
Heterotaxy, visceral, 1, X-linked
β˜…β˜†β˜†β˜†2023β†’ Residue 159
NM_003413.4(ZIC3):c.973G>A (p.Glu325Lys)Likely pathogenic
Heterotaxy, visceral, 1, X-linked;VACTERL association, X-linked, with or without hydrocephalus
β˜…β˜†β˜†β˜†2023β†’ Residue 325
NM_003413.4(ZIC3):c.627dup (p.Tyr210fs)Likely pathogenic
ZIC3-related disorder
β˜…β˜†β˜†β˜†2023β†’ Residue 210
NM_003413.4(ZIC3):c.1159_1185del (p.Pro387_Lys395del)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 387
NM_003413.4(ZIC3):c.109_112del (p.Leu37fs)Pathogenic
Heterotaxy, visceral, 1, X-linked
β˜…β˜†β˜†β˜†2023β†’ Residue 37
NM_003413.4(ZIC3):c.1079G>A (p.Cys360Tyr)Likely pathogenic
Heterotaxy, visceral, 1, X-linked
β˜…β˜†β˜†β˜†2022β†’ Residue 360
NM_003413.4(ZIC3):c.727_740del (p.Met243fs)Pathogenic
Heterotaxy, visceral, 1, X-linked
β˜…β˜†β˜†β˜†2022β†’ Residue 243
NM_003413.4(ZIC3):c.571del (p.Glu191fs)Pathogenic
Heterotaxy, visceral, 1, X-linked
β˜…β˜†β˜†β˜†2022β†’ Residue 191
View on ClinVar β†—
Related Genes
POU5F1Protein interaction95%SOX2Protein interaction95%CRIPTOProtein interaction95%LEFTY2Protein interaction95%NANOGProtein interaction95%ACVR2BProtein interaction90%
Tissue Expression6 tissues
Brain
100%
Bone Marrow
9%
Lung
0%
Ovary
0%
Heart
0%
Liver
0%
Gene Interaction Network
Click a node to explore
ZIC3POU5F1SOX2CRIPTOLEFTY2NANOGACVR2B
PROTEIN STRUCTURE
Preparing viewer…
PDB2EJ4 Β· NMR
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.65LoF Tolerant
pLIβ“˜
0.75Intermediate
Observed/Expected LoF0.33 [0.18–0.65]
RankingsWhere ZIC3 stands among ~20K protein-coding genes
  • #9,162of 20,598
    Most Researched48
  • #1,519of 5,498
    Most Pathogenic Variants41
  • #4,658of 17,882
    Most Constrained (LOEUF)0.65
Genes detectedZIC3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Human Genetics of Ventricular Septal Defect.
PMID: 38884729
Adv Exp Med Biol Β· 2024
1.00
2
ZIC2 and ZIC3 promote SWI/SNF recruitment to safeguard progression towards human primed pluripotency.
PMID: 39358345
Nat Commun Β· 2024
0.90
3
ZIC3 in Heterotaxy.
PMID: 29442328
Adv Exp Med Biol Β· 2018
0.80
4
Human Genetics of Defects of Situs.
PMID: 38884744
Adv Exp Med Biol Β· 2024
0.70
5
Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells.
PMID: 30188322
Elife Β· 2018
0.60