Zfhx3 MGI Mouse Gene Detail - MGI:99948 - zinc finger homeobox 3

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Zfhx3 Gene Detail

Symbol

Zfhx3
Name

zinc finger homeobox 3
Synonyms

A230102L03Rik, Atbf1, WBP9

Feature Type

protein coding gene
IDs

MGI:99948
NCBI Gene: 11906
Alliance

gene page
Transcription Start Sites

30 TSS

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Sequence Map

Chr8:109005975-109688272 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 8, 56.02 cM, cytoband E1
Mapping Data

4 experiments

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SNPs within 2kb

20418 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates	Select Strains
C57BL/6J	MGI_C57BL6J_99948	protein coding gene	Chr8:108669276-109688272 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0034104	protein coding gene	Chr8:111243585-111515902 (+)
A/J	MGP_AJ_G0034084	protein coding gene	Chr8:106740948-107001968 (+)
AKR/J	MGP_AKRJ_G0034010	protein coding gene	Chr8:109880692-110149447 (+)
BALB/cJ	MGP_BALBcJ_G0034077	protein coding gene	Chr8:106949066-107213347 (+)
C3H/HeJ	MGP_C3HHeJ_G0033789	protein coding gene	Chr8:110589794-110860378 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0034597	protein coding gene	Chr8:115200844-115468773 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0031539	protein coding gene	Chr8:99805228-100056391 (+)
CAST/EiJ	MGP_CASTEiJ_G0033116	protein coding gene	Chr8:110169212-110442564 (+)
CBA/J	MGP_CBAJ_G0033762	protein coding gene	Chr8:119026925-119313708 (+)
DBA/2J	MGP_DBA2J_G0033917	protein coding gene	Chr8:106078166-106338713 (+)
FVB/NJ	MGP_FVBNJ_G0033862	protein coding gene	Chr8:105015270-105278897 (+)
LP/J	MGP_LPJ_G0034008	protein coding gene	Chr8:111421451-111695610 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0033907	protein coding gene	Chr8:122110688-122382336 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0034616	protein coding gene	Chr8:109827254-110096916 (+)
PWK/PhJ	MGP_PWKPhJ_G0032818	protein coding gene	Chr8:105508437-105777084 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0032657	protein coding gene	Chr8:108548431-108817713 (+)
WSB/EiJ	MGP_WSBEiJ_G0033231	protein coding gene	Chr8:110505044-110779434 (+)

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Human Ortholog

ZFHX3, zinc finger homeobox 3

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

ZFHX3, zinc finger homeobox 3
Synonyms

ATBF1, ATBT, ATFB8, C16orf47, SCA4, ZFH-3, ZNF927
Links

HGNC:777

NCBI Gene ID: 463

UniProt: Q15911
Chr Location

16q22.2-q22.3; chr16:72782885-73891930 (-) GRCh38

MGI Vertebrate Homology

Zfhx3 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: ZFHX3
Gene Tree

Zfhx3

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Diseases

6 with human ZFHX3 associations

				Human Disease	Mouse Models
				familial atrial fibrillation IDs familial atrial fibrillation DOID:0050650 OMIM:607554 OMIM:608583 OMIM:608988 OMIM:611493 OMIM:611494 OMIM:612201 OMIM:612240 OMIM:613055 OMIM:613980 OMIM:614022 OMIM:614049 OMIM:614050 OMIM:615377 OMIM:615378 OMIM:615770 OMIM:PS608583 ORDO:334
				hepatocellular carcinoma IDs hepatocellular carcinoma DOID:684 DOID:5005 EFO:0000182 ICD10CM:C22.0 MESH:D006528 NCI:C3099 OMIM:114550 ORDO:88673 UMLS_CUI:C2239176
				lung adenocarcinoma IDs lung adenocarcinoma DOID:3910 DOID:4826 EFO:0000571 MESH:D000077192 NCI:C27745 NCI:C3512 UMLS_CUI:C0152013 UMLS_CUI:C1335060
				lung non-small cell carcinoma IDs lung non-small cell carcinoma DOID:3908 EFO:0003060 KEGG:05223 MESH:D002289 NCI:C2926 UMLS_CUI:C0007131
				prostate cancer IDs prostate cancer DOID:10283 DOID:514 ICD10CM:C61 ICD9CM:185 KEGG:05215 MESH:D011471 NCI:C3343 NCI:C7378 OMIM:176807 OMIM:300147 OMIM:300704 OMIM:601518 OMIM:602759 OMIM:608656 OMIM:608658 OMIM:609299 OMIM:609558 OMIM:610321 OMIM:610997 OMIM:611100 OMIM:611868 OMIM:611928 OMIM:611955 OMIM:611958 OMIM:611959 ORDO:1331 UMLS_CUI:C0033578 UMLS_CUI:C0376358
				spinocerebellar ataxia type 4 IDs spinocerebellar ataxia type 4 DOID:0050957 OMIM:600223 ORDO:98765 UMLS_CUI:C0752122

Click on a disease name to see all genes associated with that disease.

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Phenotype Summary

21 phenotypes from 4 alleles in 6 genetic backgrounds
1 phenotype from multigenic genotypes
1 images
22 phenotype references

Phenotype Overview

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

31
Chemically induced (ENU)

1
Gene trapped

27
Targeted

3
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

130 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a gene trapped allele exhibit normal initial pituitary development but reduced GH and TSH-beta staining within the pituitary by E17.5. Mice homozygous for a knock-out allele exhibit prenatal lethality. Mice heterozygous for the same allele exhibit partial postnatal lethality, decreased body size and prolonged conception time.

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All GO Annotations

45
GO References

11

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

1119
Tissues

178
cDNA Data

22
Literature Summary

44

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA ZFHX3

Xenbase zfhx3

ZFIN zfhx3a, zfhx3b

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All Sequences

64
RefSeq

12
UniProt

7
CCDS

CCDS22651.1

Ensembl

ENSMUSG00000038872 (Evidence)
NCBI Gene

11906

Representative Sequences				Length	Strain/Species	Flank
	genomic	11906	NCBI Gene Model \| MGI Sequence Detail	682298	C57BL/6J	± kb
	transcript	NM_007496	RefSeq \| MGI Sequence Detail	16098	C57BL/6
	polypeptide	Q61329	UniProt \| EBI \| MGI Sequence Detail	3726	Not Applicable

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UniProt

7 Sequences
Protein Ontology

PR:000017628 zinc finger homeobox protein 3

(term hierarchy)
InterPro Domains

IPR017970 Homeobox, conserved site

IPR001356 Homeobox domain

IPR009057 Homeobox-like domain superfamily

IPR003604 Matrin/U1-C-like, C2H2-type zinc finger

IPR036236 Zinc finger C2H2 superfamily

IPR013087 Zinc finger C2H2-type

IPR051968 Zinc finger homeobox transcription regulators
GlyGen

Q61329 3 sites, 1 O-linked glycan (2 sites)

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All nucleic 34

Genomic 3

cDNA 24

Primer pair 5

Other 2

Microarray probesets 7

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MGD-MRK-16751, MGI:1915410, MGI:2679553

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Summaries

All 94

Developmental Gene Expression 44

Gene Ontology 11

Phenotypes 22
Earliest

J:17985 Ido A, et al., Activation of ATBF1, a multiple-homeodomain zinc-finger gene, during neuronal differentiation of murine embryonal carcinoma cells. Dev Biol. 1994 May;163(1):184-7
Latest

J:363951 Bafna A, et al., Zinc finger homeobox-3 (ZFHX3) orchestrates genome-wide daily gene expression in the suprachiasmatic nucleus. Elife. 2025 Mar 21;14

TSS for Zfhx3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr79322	Chr8:109311679-109311683 (+)	305,706 bp
Tssr79323	Chr8:109338845-109338863 (+)	332,879 bp
Tssr79324	Chr8:109338890-109338910 (+)	332,925 bp
Tssr79325	Chr8:109364664-109364669 (+)	358,692 bp
Tssr79326	Chr8:109430086-109430133 (+)	424,135 bp
Tssr79327	Chr8:109430187-109430196 (+)	424,217 bp
Tssr79328	Chr8:109430225-109430249 (+)	424,262 bp
Tssr79329	Chr8:109430250-109430282 (+)	424,291 bp
Tssr79330	Chr8:109430302-109430342 (+)	424,347 bp
Tssr79331	Chr8:109430373-109430404 (+)	424,414 bp
Tssr79332	Chr8:109430470-109430525 (+)	424,523 bp
Tssr79333	Chr8:109430575-109430588 (+)	424,607 bp
Tssr79334	Chr8:109430706-109430739 (+)	424,748 bp
Tssr79335	Chr8:109430893-109430915 (+)	424,929 bp
Tssr79336	Chr8:109441590-109441689 (+)	435,665 bp
Tssr79337	Chr8:109441690-109441730 (+)	435,735 bp
Tssr79338	Chr8:109451359-109451365 (+)	445,387 bp
Tssr79339	Chr8:109476141-109476157 (+)	470,174 bp
Tssr79340	Chr8:109538717-109538726 (+)	532,747 bp
Tssr79341	Chr8:109565685-109565694 (+)	559,715 bp
Tssr79342	Chr8:109663709-109663713 (+)	657,736 bp
Tssr79343	Chr8:109674790-109674801 (+)	668,821 bp
Tssr79344	Chr8:109683336-109683347 (+)	677,367 bp
Tssr79345	Chr8:109683917-109683919 (+)	677,943 bp
Tssr79346	Chr8:109684495-109684499 (+)	678,522 bp
Tssr79347	Chr8:109685503-109685522 (+)	679,538 bp
Tssr79348	Chr8:109685583-109685589 (+)	679,611 bp
Tssr79349	Chr8:109686108-109686112 (+)	680,135 bp
Tssr79350	Chr8:109686195-109686219 (+)	680,232 bp
Tssr79351	Chr8:109687792-109687805 (+)	681,824 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 03/25/2025 MGI 6.24