Flrt3 MGI Mouse Gene Detail - MGI:1918686 - fibronectin leucine rich transmembrane protein 3

Symbol

Flrt3
Name

fibronectin leucine rich transmembrane protein 3
Synonyms

5530600M07Rik, C430047I10Rik, mKIAA1469

Feature Type

protein coding gene
IDs

MGI:1918686
NCBI Gene: 71436
Alliance

genome feature page
Transcription Start Sites

7 TSS

Sequence Map

Chr2:140500118-140513396 bp, - strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 69.20 cM
Mapping Data

3 experiments

SNPs within 2kb

297 from dbSNP Build 142
Strain Annotations

19

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1918686	protein coding gene	Chr2:140492834-140513396 (-)
129S1/SvImJ	ENSMUSG00200007001	protein coding gene	Chr2:137560702-137574273 (-)
A/J	ENSMUSG00195015475	protein coding gene	Chr2:137709919-137723490 (-)
AKR/J	ENSMUSG00220038088	protein coding gene	Chr2:137307306-137320876 (-)
BALB/cJ	ENSMUSG00180028181	protein coding gene	Chr2:137396853-137410423 (-)
C3H/HeJ	ENSMUSG00175031651	protein coding gene	Chr2:137942562-137956132 (-)
C57BL/6NJ	ENSMUSG00215014497	protein coding gene	Chr2:137444486-137458057 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0024369	protein coding gene	Chr2:133049744-133071008 (-)
CAST/EiJ	ENSTCUG00005010961	protein coding gene	Chr2:136616664-136630199 (-)
CBA/J	ENSMUSG00210037193	protein coding gene	Chr2:137840663-137854234 (-)
DBA/2J	ENSMUSG00185040613	protein coding gene	Chr2:137491159-137511579 (-)
FVB/NJ	ENSMUSG00205023282	protein coding gene	Chr2:136623931-136644371 (-)
JF1/MsJ	ENSUMUG00000033321	protein coding gene	Chr2:137250202-137270623 (-)
LP/J	ENSMUSG00230008470	protein coding gene	Chr2:139152293-139165863 (-)
NOD/ShiLtJ	ENSMUSG00190028372	protein coding gene	Chr2:137514456-137534921 (-)
NZO/HlLtJ	ENSMUSG00225001285	protein coding gene	Chr2:147142872-147163293 (-)
PWK/PhJ	ENSLUMG00010039924	protein coding gene	Chr2:137304052-137324474 (-)
SPRET/EiJ	ENSMSPG00010027133	protein coding gene	Chr2:139710552-139715989 (-)
WSB/EiJ	ENSIUOG00005023603	protein coding gene	Chr2:137322219-137342690 (-)

Human Ortholog

FLRT3, fibronectin leucine rich transmembrane protein 3

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

FLRT3, fibronectin leucine rich transmembrane protein 3
Synonyms

HH21
Links

HGNC:3762

NCBI Gene ID: 23767

UniProt: Q9NZU0
Chr Location

20p12.1; chr20:14322985-14337631 (-) GRCh38

MGI Vertebrate Homology

Flrt3 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: FLRT3
Gene Tree

Flrt3

Diseases

1 with human FLRT3 associations

				Human Disease	Mouse Models
				hypogonadotropic hypogonadism 21 with or without anosmia IDs hypogonadotropic hypogonadism 21 with or without anosmia DOID:0090093 ICD10CM:E23.0 OMIM:615271

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

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Phenotype Summary

20 phenotypes from 4 alleles in 6 genetic backgrounds
23 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

15
Chemically induced (other)

1
Endonuclease-mediated

2
Gene trapped

1
Radiation induced

1
Targeted

10
Genomic Mutations

2 involving Flrt3
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

42 strains or lines available
Comparison Matrix

Gene Expression + Phenotype
Recombinase Activity

Comparison Matrix Gene Expression + Recombinase Activity

Mice homozygous for a null allele exhibit embryonic lethality during organogenesis, abnormal embryonic tissue development, disrupted head formation, cardia bifida and abnormal ventral wall closure.

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All GO Annotations

75
GO References

17

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

1031
Tissues

151
cDNA Data

19
Literature Summary

26

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA FLRT3

Xenbase flrt3

ZFIN flrt3

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All Sequences

51
RefSeq

4
UniProt

2
CCDS

CCDS16806.1

Ensembl

ENSMUSG00000051379 (Evidence)
NCBI Gene

71436

			Length	Strain/Species	Flank
genomic	71436	NCBI Gene Model \| MGI Sequence Detail	13279	C57BL/6J	± kb
transcript	NM_001172160	RefSeq \| MGI Sequence Detail	4537	C57BL/6
polypeptide	Q8BGT1	UniProt \| EBI \| MGI Sequence Detail	649	Not Applicable

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UniProt

2 Sequences
Protein Ontology

PR:000007562 leucine-rich repeat transmembrane protein FLRT3

(term hierarchy)
PDB

4V2E, 4YEB
InterPro Domains

IPR000483 Cysteine-rich flanking region, C-terminal

IPR003961 Fibronectin type III

IPR001611 Leucine-rich repeat

IPR032675 Leucine-rich repeat domain superfamily

IPR000372 Leucine-rich repeat N-terminal domain

IPR003591 Leucine-rich repeat, typical subtype

IPR050333 Small Leucine-Rich Proteoglycans
GlyGen

Q8BGT1 3 sites, 2 N-linked glycans (2 sites), 1 O-linked glycan (1 site)

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All nucleic 23

cDNA 19

Primer pair 2

Other 2

Antibodies 5

Microarray probesets 7

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MGI:1924899

Summaries

All 76

Developmental Gene Expression 26

Gene Ontology 17

Phenotypes 23
Earliest

J:109968 Roderick TH, et al., Nineteen paracentric chromosomal inversions in mice. Genetics. 1974 Jan;76(1):109-17
Latest

J:374859 Torres-Cano A, et al., Spatially organized cellular communities shape functional tissue architecture in the pancreas. Sci Adv. 2025 Nov 14;11(46):eadx5791

TSS for Flrt3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr26553	Chr2:140513382-140513396 (-)	7 bp
Tssr26552	Chr2:140513360-140513378 (-)	27 bp
Tssr26551	Chr2:140513348-140513359 (-)	42 bp
Tssr26550	Chr2:140513326-140513347 (-)	59 bp
Tssr673	Chr2:140513300-140513307 (-)	92 bp
Tssr26549	Chr2:140502288-140502308 (-)	11,098 bp
Tssr26548	Chr2:140501608-140501635 (-)	11,774 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