Wdfy3 MGI Mouse Gene Detail - MGI:1096875 - WD repeat and FYVE domain containing 3

Symbol

Wdfy3
Name

WD repeat and FYVE domain containing 3
Synonyms

2610509D04Rik, Alfy, Bchs, Bwf1, D5Ertd66e, Ggtb3, mKIAA0993

Feature Type

protein coding gene
IDs

MGI:1096875
NCBI Gene: 72145
Alliance

genome feature page
Transcription Start Sites

11 TSS

Sequence Map

Chr5:101980822-102217787 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 5, 48.95 cM
Mapping Data

5 experiments

SNPs within 2kb

8201 from dbSNP Build 142
Strain Annotations

19
PCR

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1096875	protein coding gene	Chr5:101980819-102220081 (-)
129S1/SvImJ	ENSMUSG00200005019	protein coding gene	Chr5:95725323-95967551 (-)
A/J	ENSMUSG00195034595	protein coding gene	Chr5:95292145-95529132 (-)
AKR/J	ENSMUSG00220035194	protein coding gene	Chr5:94773674-95015917 (-)
BALB/cJ	ENSMUSG00180030555	protein coding gene	Chr5:95447372-95689611 (-)
C3H/HeJ	ENSMUSG00175031141	protein coding gene	Chr5:97552755-97789757 (-)
C57BL/6NJ	ENSMUSG00215010583	protein coding gene	Chr5:95368268-95605253 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0027463	protein coding gene	Chr5:94752249-94990468 (-)
CAST/EiJ	ENSTCUG00005021470	protein coding gene	Chr5:94735099-94967939 (-)
CBA/J	ENSMUSG00210030465	protein coding gene	Chr5:96303076-96540074 (-)
DBA/2J	ENSMUSG00185036620	protein coding gene	Chr5:99220464-99457471 (-)
FVB/NJ	ENSMUSG00205039066	protein coding gene	Chr5:95199012-95436002 (-)
JF1/MsJ	ENSUMUG00000006734	protein coding gene	Chr5:102180035-102420558 (-)
LP/J	ENSMUSG00230027212	protein coding gene	Chr5:103266869-103509088 (-)
NOD/ShiLtJ	ENSMUSG00190023658	protein coding gene	Chr5:95197813-95440051 (-)
NZO/HlLtJ	ENSMUSG00225012512	protein coding gene	Chr5:111036723-111275591 (-)
PWK/PhJ	ENSLUMG00010014314	protein coding gene	Chr5:94287196-94521905 (-)
SPRET/EiJ	ENSMSPG00010022825	protein coding gene	Chr5:97205467-97410219 (-)
WSB/EiJ	ENSIUOG00005030209	protein coding gene	Chr5:97925920-98162807 (-)

Human Ortholog

WDFY3, WD repeat and FYVE domain containing 3

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

WDFY3, WD repeat and FYVE domain containing 3
Synonyms

ALFY, BCHS, MCPH18, ZFYVE25
Links

HGNC:20751

NCBI Gene ID: 23001

UniProt: Q8IZQ1
Chr Location

4q21.23; chr4:84668765-84966690 (-) GRCh38

MGI Vertebrate Homology

Wdfy3 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: WDFY3
Gene Tree

Wdfy3

Diseases

1 with Wdfy3 mouse models; 1 with human WDFY3 associations

Human Disease

Mouse Models

autism spectrum disorder

IDs

View 2 models

primary autosomal dominant microcephaly 18

IDs

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

Mutations/Alleles

2 with disease annotations

References

1 with disease annotations

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Phenotype Summary

59 phenotypes from 5 alleles in 5 genetic backgrounds
7 images
33 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

92
Chemically induced (ENU)

2
Chemically induced (other)

1
Endonuclease-mediated

3
Gene trapped

77
Radiation induced

1
Spontaneous

1
Targeted

6
Transposon induced

1
Genomic Mutations

3 involving Wdfy3
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

212 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for hypomorphic mutations of this gene exhibit perinatal lethality, altered neural progenitor divisions and neuronal migration, a regionally enlarged cerebral cortex, and focal cortical dysplasia. Homozygotes for a null allele show embryonic and neonatal lethality, congenital heart defects including VSD, overriding aorta and DORV, thin ventricular wall, dilated ventricles, and disorganized ventricular trabeculation.

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All GO Annotations

32
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

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

704
Tissues

23
cDNA Data

13
Literature Summary

10

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase wdfy3

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All Sequences

97
RefSeq

29
UniProt

7
CCDS

CCDS19473.1

Ensembl

ENSMUSG00000043940 (Evidence)
NCBI Gene

72145

			Length	Strain/Species	Flank
genomic	ENSMUSG00000043940	Ensembl Gene Model \| MGI Sequence Detail	236966	C57BL/6J	± kb
transcript	ENSMUST00000174598	Ensembl \| MGI Sequence Detail	10581	Not Applicable
polypeptide	ENSMUSP00000134244	Ensembl \| MGI Sequence Detail	3526	Not Applicable

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UniProt

7 Sequences
Protein Ontology

PR:000031421 WD repeat and FYVE domain-containing protein 3

(term hierarchy)
EC

2.4.1.38
InterPro Domains

IPR056252 Alfy-like, armadillo-like repeat domain

IPR011989 Armadillo-like helical

IPR016024 Armadillo-type fold

IPR000409 BEACH domain

IPR036372 BEACH domain superfamily

IPR051944 Blue cheese protein homologue

IPR013320 Concanavalin A-like lectin/glucanase domain superfamily

IPR000306 FYVE zinc finger

IPR023362 PH-BEACH domain

IPR011993 PH-like domain superfamily

IPR001680 WD40 repeat

IPR019775 WD40 repeat, conserved site

IPR036322 WD40-repeat-containing domain superfamily

IPR015943 WD40/YVTN repeat-like-containing domain superfamily

IPR011011 Zinc finger, FYVE/PHD-type

IPR017455 Zinc finger, FYVE-related

IPR013083 Zinc finger, RING/FYVE/PHD-type
GlyGen

Q6VNB8 12 sites, 1 N-linked glycan (1 site), 1 O-linked glycan (7 sites)

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All nucleic 22

cDNA 18

Primer pair 4

Antibodies 1

Microarray probesets 7

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MGI:1098710, MGI:1919395, MGI:2141186

Summaries

All 80

Developmental Gene Expression 10

Diseases 1

Gene Ontology 11

Phenotypes 33
Earliest

J:134667 Roderick TH, et al., Two radiation-induced chromosomal inversions in mice (Mus musculus). Proc Natl Acad Sci U S A. 1970 Oct;67(2):961-7
Latest

J:373754 Croce KR, et al., A rare genetic variant confers resistance to neurodegeneration across multiple neurological disorders by augmenting selective autophagy. Neuron. 2025 Sep 12;

TSS for Wdfy3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr52139	Chr5:102217771-102217806 (-)	-2 bp
Tssr52138	Chr5:102200905-102200953 (-)	16,858 bp
Tssr52137	Chr5:102200884-102200899 (-)	16,895 bp
Tssr52136	Chr5:102166255-102166259 (-)	51,530 bp
Tssr52135	Chr5:102070445-102070495 (-)	147,317 bp
Tssr52134	Chr5:101999408-101999418 (-)	218,374 bp
Tssr52133	Chr5:101999389-101999403 (-)	218,391 bp
Tssr52132	Chr5:101999373-101999383 (-)	218,409 bp
Tssr52131	Chr5:101999366-101999371 (-)	218,418 bp
Tssr52130	Chr5:101999354-101999361 (-)	218,429 bp
Tssr52129	Chr5:101983471-101983476 (-)	234,313 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 09/01/2026 MGI 6.24