Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	7547
Gene name	Zic family zinc finger 3
Gene symbol	ZIC3
Synonyms (NCBI Gene)	HTXHTX1VACTERLXZNF203
Chromosome	X
Chromosome location	Xq26.3
Summary	This gene encodes a member of the ZIC family of C2H2-type zinc finger proteins. This nuclear protein probably functions as a transcription factor in early stages of left-right body axis formation. Mutations in this gene cause X-linked visceral heterotaxy,

Show/Hide all (22)

SNP ID	Visualize variation	Clinical significance	Consequence
rs104894960	C>T	Pathogenic	Coding sequence variant, stop gained
rs104894961	G>C	Pathogenic	Coding sequence variant, missense variant
rs104894962	A>G	Pathogenic	Coding sequence variant, missense variant
rs122462165	C>T	Pathogenic	Coding sequence variant, missense variant
rs122462166	C>A	Pathogenic	Coding sequence variant, stop gained
rs122463167	T>A	Pathogenic	Coding sequence variant, missense variant
rs122463168	T>G	Pathogenic	Coding sequence variant, missense variant
rs143990850	G>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs147232392	G>A,T	Conflicting-interpretations-of-pathogenicity, likely-benign, benign-likely-benign, benign	Missense variant, coding sequence variant
rs387906498	A>T	Pathogenic	Stop gained, coding sequence variant
rs398122850	->GCCGCC	Pathogenic	Inframe insertion, coding sequence variant
rs748325646	CGCCGCCGCCGCCGC>-,CGC,CGCCGC,CGCCGCCGC,CGCCGCCGCCGC,CGCCGCCGCCGCCGCCGC,CGCCGCCGCCGCCGCCGCCGC,CGCCGCCGCCGCCGCCGCCGCCGC,CGCCGCCGCCGCCGCCGCCGCCGCCGC	Likely-benign, uncertain-significance, benign, conflicting-interpretations-of-pathogenicity	Inframe insertion, inframe deletion, coding sequence variant
rs763534805	G>A,C	Likely-pathogenic	Coding sequence variant, missense variant
rs886041111	G>C	Likely-pathogenic	Missense variant, coding sequence variant
rs886042663	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs1203069392	C>A,T	Pathogenic	Missense variant, coding sequence variant, stop gained
rs1556029841	ACTT>-	Pathogenic	Frameshift variant, coding sequence variant
rs1569345504	C>A	Pathogenic	Coding sequence variant, stop gained
rs1569345723	->G	Pathogenic	Coding sequence variant, frameshift variant
rs1569345742	CATACCGCCCAGTGGCC>-	Pathogenic	Coding sequence variant, frameshift variant
rs1602742808	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs1602743059	C>T	Likely-pathogenic	Coding sequence variant, stop gained

Show/Hide all (75)

miRTarBase ID	miRNA	Experiments	Reference
MIRT000976	hsa-miR-155-5p	Luciferase reporter assay	18367535
MIRT000976	hsa-miR-155-5p	Luciferase reporter assay	18367535
MIRT000976	hsa-miR-155-5p	Luciferase reporter assay	19177201
MIRT000976	hsa-miR-155-5p	Review	20026422
MIRT000976	hsa-miR-155-5p	Other	20584899
MIRT1513422	hsa-miR-1224-5p	CLIP-seq
MIRT1513423	hsa-miR-1227	CLIP-seq
MIRT1513424	hsa-miR-1271	CLIP-seq
MIRT1513425	hsa-miR-1304	CLIP-seq
MIRT1513426	hsa-miR-155	CLIP-seq
MIRT1513427	hsa-miR-182	CLIP-seq
MIRT1513428	hsa-miR-208a	CLIP-seq
MIRT1513429	hsa-miR-208b	CLIP-seq
MIRT1513430	hsa-miR-219-2-3p	CLIP-seq
MIRT1513431	hsa-miR-2964a-3p	CLIP-seq
MIRT1513432	hsa-miR-3117-5p	CLIP-seq
MIRT1513433	hsa-miR-3616-5p	CLIP-seq
MIRT1513434	hsa-miR-3617	CLIP-seq
MIRT1513435	hsa-miR-3647-5p	CLIP-seq
MIRT1513436	hsa-miR-3653	CLIP-seq
MIRT1513437	hsa-miR-3658	CLIP-seq
MIRT1513438	hsa-miR-3688-3p	CLIP-seq
MIRT1513439	hsa-miR-383	CLIP-seq
MIRT1513440	hsa-miR-3915	CLIP-seq
MIRT1513441	hsa-miR-3928	CLIP-seq
MIRT1513442	hsa-miR-4261	CLIP-seq
MIRT1513443	hsa-miR-4264	CLIP-seq
MIRT1513444	hsa-miR-4267	CLIP-seq
MIRT1513445	hsa-miR-4426	CLIP-seq
MIRT1513446	hsa-miR-4432	CLIP-seq
MIRT1513447	hsa-miR-4457	CLIP-seq
MIRT1513448	hsa-miR-455-5p	CLIP-seq
MIRT1513449	hsa-miR-4647	CLIP-seq
MIRT1513450	hsa-miR-4662b	CLIP-seq
MIRT1513451	hsa-miR-4680-3p	CLIP-seq
MIRT1513452	hsa-miR-4689	CLIP-seq
MIRT1513453	hsa-miR-4700-3p	CLIP-seq
MIRT1513454	hsa-miR-4738-3p	CLIP-seq
MIRT1513455	hsa-miR-4772-5p	CLIP-seq
MIRT1513456	hsa-miR-4797-3p	CLIP-seq
MIRT1513457	hsa-miR-4803	CLIP-seq
MIRT1513458	hsa-miR-499-5p	CLIP-seq
MIRT1513459	hsa-miR-513b	CLIP-seq
MIRT1513460	hsa-miR-564	CLIP-seq
MIRT1513461	hsa-miR-573	CLIP-seq
MIRT1513462	hsa-miR-576-3p	CLIP-seq
MIRT1513463	hsa-miR-584	CLIP-seq
MIRT1513464	hsa-miR-605	CLIP-seq
MIRT1513465	hsa-miR-622	CLIP-seq
MIRT1513466	hsa-miR-641	CLIP-seq
MIRT1513467	hsa-miR-96	CLIP-seq
MIRT1513422	hsa-miR-1224-5p	CLIP-seq
MIRT1513425	hsa-miR-1304	CLIP-seq
MIRT1513440	hsa-miR-3915	CLIP-seq
MIRT1513441	hsa-miR-3928	CLIP-seq
MIRT1513452	hsa-miR-4689	CLIP-seq
MIRT1513422	hsa-miR-1224-5p	CLIP-seq
MIRT1513425	hsa-miR-1304	CLIP-seq
MIRT1513426	hsa-miR-155	CLIP-seq
MIRT2154750	hsa-miR-3668	CLIP-seq
MIRT1513440	hsa-miR-3915	CLIP-seq
MIRT1513441	hsa-miR-3928	CLIP-seq
MIRT1513447	hsa-miR-4457	CLIP-seq
MIRT1513452	hsa-miR-4689	CLIP-seq
MIRT1513459	hsa-miR-513b	CLIP-seq
MIRT1513422	hsa-miR-1224-5p	CLIP-seq
MIRT1513425	hsa-miR-1304	CLIP-seq
MIRT1513426	hsa-miR-155	CLIP-seq
MIRT1513438	hsa-miR-3688-3p	CLIP-seq
MIRT1513440	hsa-miR-3915	CLIP-seq
MIRT1513441	hsa-miR-3928	CLIP-seq
MIRT1513442	hsa-miR-4261	CLIP-seq
MIRT1513447	hsa-miR-4457	CLIP-seq
MIRT1513452	hsa-miR-4689	CLIP-seq
MIRT1513459	hsa-miR-513b	CLIP-seq

Show/Hide all (71)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000977	Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	IEA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA	17764085
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IDA	17764085
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IEA
GO:0001501	Process	Skeletal system development	IEA
GO:0001840	Process	Neural plate development	IEA
GO:0001947	Process	Heart looping	IEA
GO:0001947	Process	Heart looping	IMP	9354794
GO:0003228	Process	Atrial cardiac muscle tissue development	IEA
GO:0003677	Function	DNA binding	IEA
GO:0003700	Function	DNA-binding transcription factor activity	IDA	17764085
GO:0003700	Function	DNA-binding transcription factor activity	IEA
GO:0003713	Function	Transcription coactivator activity	IEA
GO:0005515	Function	Protein binding	IPI	17764085, 18716025
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	ISS
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	ISS
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IEA
GO:0007224	Process	Smoothened signaling pathway	IEA
GO:0007368	Process	Determination of left/right symmetry	IEA
GO:0007368	Process	Determination of left/right symmetry	IMP	9354794
GO:0007369	Process	Gastrulation	IEA
GO:0007389	Process	Pattern specification process	IEA
GO:0007399	Process	Nervous system development	IEA
GO:0007417	Process	Central nervous system development	IBA
GO:0007498	Process	Mesoderm development	IEA
GO:0007507	Process	Heart development	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0009880	Process	Embryonic pattern specification	IEA
GO:0009952	Process	Anterior/posterior pattern specification	IEA
GO:0010467	Process	Gene expression	IEA
GO:0019827	Process	Stem cell population maintenance	IEA
GO:0021766	Process	Hippocampus development	IEA
GO:0021772	Process	Olfactory bulb development	IEA
GO:0030154	Process	Cell differentiation	IEA
GO:0030182	Process	Neuron differentiation	IEA
GO:0030324	Process	Lung development	IMP	9354794
GO:0030718	Process	Germ-line stem cell population maintenance	IEA
GO:0030900	Process	Forebrain development	IEA
GO:0035108	Process	Limb morphogenesis	IEA
GO:0035283	Process	Central nervous system segmentation	IEA
GO:0035469	Process	Determination of pancreatic left/right asymmetry	IMP	9354794
GO:0035545	Process	Determination of left/right asymmetry in nervous system	IEA
GO:0042473	Process	Outer ear morphogenesis	IEA
GO:0042789	Process	MRNA transcription by RNA polymerase II	IEA
GO:0043565	Function	Sequence-specific DNA binding	IDA	17764085
GO:0045893	Process	Positive regulation of DNA-templated transcription	IEA
GO:0045893	Process	Positive regulation of DNA-templated transcription	ISS
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IBA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IDA	17764085
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0048318	Process	Axial mesoderm development	IEA
GO:0048339	Process	Paraxial mesoderm development	IEA
GO:0048863	Process	Stem cell differentiation	IEA
GO:0060324	Process	Face development	IEA
GO:0060972	Process	Left/right pattern formation	IEA
GO:0070986	Process	Left/right axis specification	IEA
GO:0071907	Process	Determination of digestive tract left/right asymmetry	IMP	9354794
GO:0071910	Process	Determination of liver left/right asymmetry	IMP	9354794
GO:0090009	Process	Primitive streak formation	IEA
GO:0098727	Process	Maintenance of cell number	IEA
GO:1904888	Process	Cranial skeletal system development	IEA
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536

MIM	HGNC	e!Ensembl
300265	12874	ENSG00000156925

O60481

Protein name

Zinc finger protein ZIC 3 (Zinc finger protein 203) (Zinc finger protein of the cerebellum 3)

Protein function

Acts as a transcriptional activator. Required in the earliest stages in both axial midline development and left-right (LR) asymmetry specification. Binds to the minimal GLI-consensus sequence 5'-GGGTGGTC-3'.

PDB

2EJ4 , 2RPC

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF18366	zf_ZIC	244 → 290	Zic proteins zinc finger domain	Domain
PF00096	zf-C2H2	295 → 322	Zinc finger, C2H2 type	Domain
PF00096	zf-C2H2	328 → 352	Zinc finger, C2H2 type	Domain
PF00096	zf-C2H2	358 → 382	Zinc finger, C2H2 type	Domain
PF00096	zf-C2H2	388 → 410	Zinc finger, C2H2 type	Domain

Sequence

MTMLLDGGPQFPGLGVGSFGAPRHHEMPNREPAGMGLNPFGDSTHAAAAAAAAAAFKLSP
AAAHDLSSGQSSAFTPQGSGYANALGHHHHHHHHHHHTSQVPSYGGAASAAFNSTREFLF
RQRSSGLSEAASGGGQHGLFAGSASSLHAPAGIPEPPSYLLFPGLHEQGAGHPSPTGHVD
NNQVHLGLRGELFGRADPYRPVASPRTDPYAAGAQFPNYSPMNMNMGVNVAAHHGPGAFF
RYMRQPIKQELSCKWIDEAQLSRPKKSCDRTFSTMHELVTHVTMEHVGGPEQNNHVCYWE
ECPREGKSFKAKYKLVNHIRVHTGEKPFPCPFPGCGKIFARSENLKIHKRTHTGEKPFKC
EFEGCDRRFANSSDRKKHMHVHTSDKPYICKVCDKSYTHPSSLRKHMKVHESQGSDSSPA
ASSGYESSTPPAIASANSKDTTKTPSAVQTSTSHNPGLPPNFNEWYV

Sequence length

467

Interactions

View interactions

	KEGG		Reactome
	Signaling pathways regulating pluripotency of stem cells		POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation Transcriptional regulation of pluripotent stem cells

196

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Congenital heart defects, multiple types, 1, X-linked	Pathogenic	rs387906498	RCV000012188
Heterotaxy, visceral, 1, X-linked	Pathogenic; Likely pathogenic	rs2124184204, rs2124185586, rs2124184171, rs2521149558, rs2521154725, rs2521150121, rs2521150898, rs886041111, rs122462165, rs122462166, rs104894960, rs104894961, rs104894962, rs2124184319, rs122463168 View all (12 more)	RCV001389078 RCV001387447 RCV001935541 RCV002286594 RCV002470296 RCV003053786 RCV003039444 RCV000258959 RCV000012186 RCV000012187 RCV000012189 RCV000012190 RCV000012191 RCV000012193 RCV000012194 RCV003513703 RCV003625225 RCV003989886 RCV000540603 RCV000754887 RCV000754888 RCV000754889 RCV000754890 RCV000691248 RCV000800000 RCV001007872 RCV001057896 RCV001223598
VACTERL association, X-linked, with or without hydrocephalus	Likely pathogenic; Pathogenic	rs2124185586, rs398122850	RCV001420556 RCV000022847
ZIC3-related disorder	Likely pathogenic	rs2521149676	RCV003397374

Show/Hide Unknown Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Congenital heart defects 1, nonsyndromic, 1	Benign; Likely benign; Conflicting classifications of pathogenicity; Uncertain significance	rs147232392, rs104894963, rs78870836, rs184855783, rs1022475218, rs779221820, rs41300285, rs772508899, rs113057036, rs183286584, rs1057515786, rs12387258, rs899320157, rs1057515787	RCV000360572 RCV000370424 RCV000274738 RCV000371410 RCV000340786 RCV000291067 RCV000269010 RCV000272400 RCV000294271 RCV000398018 RCV000369849 RCV000377698 RCV000401459 RCV000397270

Show/Hide Text Mining Associations (18)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Breast Neoplasms	Associate	29333926
Cardiovascular Abnormalities	Associate	21864452, 35474353
Chromosome Aberrations	Associate	27821535
Double Outlet Right Ventricle	Associate	29866040
Facial Asymmetry	Associate	9311745
Glioblastoma	Associate	34475426
Glioma	Associate	34475426
Glycosuria Renal	Associate	34338422
Heart Defects Congenital	Associate	22318994, 26014430
Heart Diseases	Associate	21864452, 26014430
Heterotaxy Syndrome	Associate	21864452, 27821535, 31167209, 9311745
Heterotaxy visceral X linked	Associate	27821535
Hodgkin Disease	Associate	19177201
Laterality Defects Autosomal Dominant	Associate	35474353
Prolactinoma	Associate	25313736
Severe combined immunodeficiency due to adenosine deaminase deficiency	Associate	31167209
VACTERL association	Associate	34338422
VATER association	Associate	34338422

ZIC3 (Zic family zinc finger 3)