Wnt3a MGI Mouse Gene Detail - MGI:98956 - wingless-type MMTV integration site family, member 3A

Symbol

Wnt3a
Name

wingless-type MMTV integration site family, member 3A
Synonyms

Wnt-3a

Feature Type

protein coding gene
IDs

MGI:98956
NCBI Gene: 22416
Alliance

genome feature page
Transcription Start Sites

1 TSS

Sequence Map

Chr11:59138859-59181578 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 11, 37.17 cM
Mapping Data

27 experiments

SNPs within 2kb

1174 from dbSNP Build 142
Strain Annotations

19
RFLP

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_98956	protein coding gene	Chr11:59138859-59181579 (-)
129S1/SvImJ	ENSMUSG00200035251	protein coding gene	Chr11:56146199-56188919 (-)
A/J	ENSMUSG00195036249	protein coding gene	Chr11:56074559-56117441 (-)
AKR/J	ENSMUSG00220047785	protein coding gene	Chr11:56242919-56285962 (-)
BALB/cJ	ENSMUSG00180044445	protein coding gene	Chr11:56162434-56205186 (-)
C3H/HeJ	ENSMUSG00175040861	protein coding gene	Chr11:56109730-56152615 (-)
C57BL/6NJ	ENSMUSG00215038774	protein coding gene	Chr11:55929783-55972517 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0016432	protein coding gene	Chr11:54062807-54105615 (-)
CAST/EiJ	ENSTCUG00005046779	protein coding gene	Chr11:55654259-55697389 (-)
CBA/J	ENSMUSG00210034485	protein coding gene	Chr11:55961110-56003987 (-)
DBA/2J	ENSMUSG00185038141	protein coding gene	Chr11:56146060-56188804 (-)
FVB/NJ	ENSMUSG00205022207	protein coding gene	Chr11:56014752-56057654 (-)
JF1/MsJ	ENSUMUG00000008256	protein coding gene	Chr11:56492885-56535787 (-)
LP/J	ENSMUSG00230050114	protein coding gene	Chr11:57354204-57396930 (-)
NOD/ShiLtJ	ENSMUSG00190031359	protein coding gene	Chr11:56215648-56258685 (-)
NZO/HlLtJ	ENSMUSG00225031575	protein coding gene	Chr11:59353476-59396199 (-)
PWK/PhJ	ENSLUMG00010025415	protein coding gene	Chr11:55960718-56003634 (-)
SPRET/EiJ	ENSMSPG00010038040	protein coding gene	Chr11:56734256-56776990 (-)
WSB/EiJ	ENSIUOG00005029251	protein coding gene	Chr11:56013593-56056651 (-)

Human Ortholog

WNT3A, Wnt family member 3A

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

WNT3A, Wnt family member 3A
Links

HGNC:15983

NCBI Gene ID: 89780

UniProt: P56704
Chr Location

1q42.13; chr1:228006924-228061271 (+) GRCh38

MGI Vertebrate Homology

Wnt3a stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: WNT3A
Gene Tree

Wnt3a

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Phenotype Summary

67 phenotypes from 6 alleles in 11 genetic backgrounds
29 phenotypes from multigenic genotypes
2 images
106 phenotype references

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

23
Chemically induced (ENU)

1
Chemically induced (other)

1
Endonuclease-mediated

6
Gene trapped

7
Spontaneous

1
Targeted

7
Genomic Mutations

1 involving Wnt3a
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

31 strains or lines available
Comparison Matrix

Gene Expression + Phenotype
Recombinase Activity

Comparison Matrix Gene Expression + Recombinase Activity

Homozygous null mutants die at embryonic day 10.5-12.5 with failed development of caudal somites, notochord and structures rostral to hindlimbs. Homozygotes for a hypomorphic allele have vertebral defects and a short tail due to loss of caudal vertebrae.

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All GO Annotations

178
GO References

91

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

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

1741
Tissues

626
cDNA Data

22
Literature Summary

349

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GENSAT

GEO

Expression Atlas
Other Vertebrate Links

GEISHA WNT3A

Xenbase wnt3a

ZFIN wnt3a

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All Sequences

28
RefSeq

2
UniProt

1
CCDS

CCDS24766.1

Ensembl

ENSMUSG00000009900 (Evidence)
NCBI Gene

22416

			Length	Strain/Species	Flank
genomic	ENSMUSG00000009900	Ensembl Gene Model \| MGI Sequence Detail	42720	C57BL/6J	± kb
transcript	ENSMUST00000010044	Ensembl \| MGI Sequence Detail	2761	Not Applicable
polypeptide	ENSMUSP00000010044	Ensembl \| MGI Sequence Detail	352	Not Applicable

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UniProt

1 Sequence
Protein Ontology

PR:000017443 protein Wnt-3a

(term hierarchy)
InterPro Domains

IPR005817 Wnt

IPR009141 Wnt-3 protein

IPR043158 Wnt, C-terminal domain

IPR018161 Wnt protein, conserved site
GlyGen

P27467 2 sites

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All nucleic 106

Genomic 3

cDNA 26

Primer pair 33

Other 44

Antibodies 3

Microarray probesets 3

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MGD-MRK-15417, MGD-MRK-15441, MGD-MRK-15451

Summaries

All 711

Developmental Gene Expression 349

Gene Ontology 91

Phenotypes 106
Earliest

J:13062 HESTON WE, The 'vestigial tail' mouse; a new recessive mutation. J Hered. 1951 Mar-Apr;42(2):71-4
Latest

J:383143 Singh A, et al., Cajal-Retzius fate specification is disrupted by constitutive activation of beta-Catenin in hem progenitors. Development. 2026 Apr 1;153(7):dev205072

TSS for Wnt3a:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr108216	Chr11:59181572-59181584 (-)	0 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 09/08/2026 MGI 6.24