Lhx1 MGI Mouse Gene Detail - MGI:99783

Symbol

Lhx1
Name

LIM homeobox protein 1
Synonyms

Lim1

Feature Type

protein coding gene
IDs

MGI:99783
NCBI Gene: 16869
Alliance

genome feature page
Transcription Start Sites

4 TSS

Sequence Map

Chr11:84409110-84416361 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 11, 51.31 cM
Mapping Data

4 experiments

SNPs within 2kb

184 from dbSNP Build 142
Strain Annotations

19
RFLP

3

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_99783	protein coding gene	Chr11:84408801-84416361 (-)
129S1/SvImJ	ENSMUSG00200046949	protein coding gene	Chr11:81548826-81556059 (-)
A/J	ENSMUSG00195041118	protein coding gene	Chr11:81403328-81410561 (-)
AKR/J	ENSMUSG00220047324	protein coding gene	Chr11:81618119-81625368 (-)
BALB/cJ	ENSMUSG00180039416	protein coding gene	Chr11:81599705-81606958 (-)
C3H/HeJ	ENSMUSG00175036736	protein coding gene	Chr11:81550266-81557499 (-)
C57BL/6NJ	ENSMUSG00215041481	protein coding gene	Chr11:81183354-81190605 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0016895	protein coding gene	Chr11:79757164-79761810 (-)
CAST/EiJ	ENSTCUG00005043136	protein coding gene	Chr11:81117208-81124213 (-)
CBA/J	ENSMUSG00210045389	protein coding gene	Chr11:81367903-81375136 (-)
DBA/2J	ENSMUSG00185018324	protein coding gene	Chr11:81699737-81707021 (-)
FVB/NJ	ENSMUSG00205042040	protein coding gene	Chr11:81487327-81494579 (-)
JF1/MsJ	ENSUMUG00000008195	protein coding gene	Chr11:82020975-82028255 (-)
LP/J	ENSMUSG00230026292	protein coding gene	Chr11:82717990-82725223 (-)
NOD/ShiLtJ	ENSMUSG00190017623	protein coding gene	Chr11:81699569-81706820 (-)
NZO/HlLtJ	ENSMUSG00225039086	protein coding gene	Chr11:84827701-84834953 (-)
PWK/PhJ	ENSLUMG00010023132	protein coding gene	Chr11:81522493-81529788 (-)
SPRET/EiJ	ENSMSPG00010040298	protein coding gene	Chr11:81986403-81993666 (-)
WSB/EiJ	ENSIUOG00005006759	protein coding gene	Chr11:81507950-81515182 (-)

Human Ortholog

LHX1, LIM homeobox 1

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

LHX1, LIM homeobox 1
Synonyms

LIM-1, LIM1
Links

HGNC:6593

NCBI Gene ID: 3975

UniProt: P48742
Chr Location

17q12; chr17:36936784-36944612 (+) GRCh38

MGI Vertebrate Homology

Lhx1 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: LHX1
Gene Tree

Lhx1

less

References

1 with disease annotations

less

Phenotype Summary

80 phenotypes from 8 alleles in 11 genetic backgrounds
13 phenotypes from multigenic genotypes
61 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

1
Targeted

12
Transgenic

1
Genomic Mutations

3 involving Lhx1
Incidental Mutations

APF
Find Mice (IMSR)

21 strains or lines available
Comparison Matrix

Gene Expression + Phenotype
Recombinase Activity

Comparison Matrix Gene Expression + Recombinase Activity

Homozygotes for targeted null mutations are small, fail to develop head structures anterior to rhombomere 3 in the hindbrain, lack kidneys and gonads, and show aberrant trajectories of limb motor axons. Most mutants die around embryonic day 10.

less

All GO Annotations

109
GO References

28

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.

less

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

2631
Tissues

704
cDNA Data

42
Literature Summary

549

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GENSAT

GEO

Expression Atlas
Other Vertebrate Links

GEISHA LHX1

Xenbase lhx1

ZFIN lhx1a, lhx1b

less

All Sequences

48
RefSeq

2
UniProt

7
CCDS

CCDS25187.1

Ensembl

ENSMUSG00000018698 (Evidence)
NCBI Gene

16869

			Length	Strain/Species	Flank
genomic	ENSMUSG00000018698	Ensembl Gene Model \| MGI Sequence Detail	7252	C57BL/6J	± kb
transcript	ENSMUST00000018842	Ensembl \| MGI Sequence Detail	3846	Not Applicable
polypeptide	ENSMUSP00000018842	Ensembl \| MGI Sequence Detail	406	Not Applicable

less

UniProt

7 Sequences
Protein Ontology

PR:000009791 LIM/homeobox protein Lhx1

(term hierarchy)
InterPro Domains

IPR017970 Homeobox, conserved site

IPR001356 Homeodomain

IPR009057 Homeodomain-like superfamily

IPR049618 Lhx1/5, LIM domain 1

IPR049619 Lhx1/5, LIM domain 2

IPR050453 LIM/homeobox transcription factors

IPR001781 Zinc finger, LIM-type

less

All nucleic 110

Genomic 3

cDNA 50

Primer pair 19

Other 38

Antibodies 18

Microarray probesets 4

less

MGD-MRK-16569

Summaries

All 631

Developmental Gene Expression 549

Diseases 1

Gene Ontology 28

Phenotypes 61
Earliest

J:137335 Roderick TH, Chromosomal inversions in studies of mammalian mutagenesis. Genetics. 1979 May;92(1 Pt 1 Suppl):s121-6
Latest

J:390120 Trowe MO, et al., Mesenchymal WNT signaling coordinates epithelial and mesenchymal differentiation in the developing murine ureter. Cell Commun Signal. 2026 Jul 21;24(1)

TSS for Lhx1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr109767	Chr11:84416340-84416368 (-)	7 bp
Tssr109766	Chr11:84415681-84415696 (-)	672 bp
Tssr109765	Chr11:84410099-84410112 (-)	6,255 bp
Tssr109764	Chr11:84409873-84409885 (-)	6,482 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