Lmx1a MGI Mouse Gene Detail - MGI:1888519 - LIM homeobox transcription factor 1 alpha

Symbol

Lmx1a
Name

LIM homeobox transcription factor 1 alpha
Synonyms

Lmx1.1, shaker short-tail

Feature Type

protein coding gene
IDs

MGI:1888519
NCBI Gene: 110648
Alliance

genome feature page
Transcription Start Sites

6 TSS

Sequence Map

Chr1:167516806-167676310 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 1, 75.08 cM
Mapping Data

14 experiments

SNPs within 2kb

4709 from dbSNP Build 142
Strain Annotations

19

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1888519	protein coding gene	Chr1:167515864-167676310 (+)
129S1/SvImJ	ENSMUSG00200043438	protein coding gene	Chr1:165022050-165181574 (+)
A/J	ENSMUSG00195044408	protein coding gene	Chr1:164331205-164479370 (+)
AKR/J	ENSMUSG00220025518	protein coding gene	Chr1:164053299-164212830 (+)
BALB/cJ	ENSMUSG00180043591	protein coding gene	Chr1:164574996-164734507 (+)
C3H/HeJ	ENSMUSG00175047179	protein coding gene	Chr1:164678460-164837973 (+)
C57BL/6NJ	ENSMUSG00215043538	protein coding gene	Chr1:164456568-164616082 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0014828	protein coding gene	Chr1:158039005-158185139 (+)
CAST/EiJ	ENSTCUG00005044264	protein coding gene	Chr1:163034503-163182996 (+)
CBA/J	ENSMUSG00210039039	protein coding gene	Chr1:164539595-164687323 (+)
DBA/2J	ENSMUSG00185011604	protein coding gene	Chr1:168756067-168903861 (+)
FVB/NJ	ENSMUSG00205025903	protein coding gene	Chr1:163542887-163691064 (+)
JF1/MsJ	ENSUMUG00000004298	protein coding gene	Chr1:167909231-168063436 (+)
LP/J	ENSMUSG00230021874	protein coding gene	Chr1:168409848-168569328 (+)
NOD/ShiLtJ	ENSMUSG00190026688	protein coding gene	Chr1:164337115-164485267 (+)
NZO/HlLtJ	ENSMUSG00225003529	protein coding gene	Chr1:171999340-172158828 (+)
PWK/PhJ	ENSLUMG00010029222	protein coding gene	Chr1:163285702-163432984 (+)
SPRET/EiJ	ENSMSPG00010043457	protein coding gene	Chr1:166804649-166949056 (+)
WSB/EiJ	ENSIUOG00005034510	protein coding gene	Chr1:163770049-163918120 (+)

Human Ortholog

LMX1A, LIM homeobox transcription factor 1 alpha

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

LMX1A, LIM homeobox transcription factor 1 alpha
Synonyms

DFNA7, LMX1, LMX1.1
Links

HGNC:6653

NCBI Gene ID: 4009

UniProt: Q8TE12
Chr Location

1q23.3; chr1:165201867-165356715 (-) GRCh38

MGI Vertebrate Homology

Lmx1a stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: LMX1A
Gene Tree

Lmx1a

Diseases

1 with human LMX1A associations

				Human Disease	Mouse Models
				autosomal dominant nonsyndromic deafness 7 IDs autosomal dominant nonsyndromic deafness 7 DOID:0110591 ICD10CM:H90.3 OMIM:601412

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

Mutations/Alleles

1 with disease annotations

References

1 with disease annotations

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Phenotype Summary

83 phenotypes from 14 alleles in 16 genetic backgrounds
20 phenotypes from multigenic genotypes
4 images
68 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

29
Chemically induced (other)

2
Endonuclease-mediated

4
Spontaneous

16
Targeted

7
Genomic Mutations

2 involving Lmx1a
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

23 strains or lines available
Comparison Matrix

Gene Expression + Phenotype
Recombinase Activity

Comparison Matrix Gene Expression + Recombinase Activity

Mutations in the dreher locus produce neurological and skeletal abnormalities, inner ear defects, and belly spotting. Deafness and hypoplasia of Mullerian duct derivatives are also reported for some alleles. Homozygous null mice have fewer dopaminergic neurons.

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All GO Annotations

41
GO References

14

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

1201
Tissues

274
cDNA Data

21
Literature Summary

192

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase lmx1a

ZFIN lmx1a

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All Sequences

40
RefSeq

8
UniProt

2
CCDS

CCDS15460.1

Ensembl

ENSMUSG00000026686 (Evidence)
NCBI Gene

110648

			Length	Strain/Species	Flank
genomic	ENSMUSG00000026686	Ensembl Gene Model \| MGI Sequence Detail	159505	C57BL/6J	± kb
transcript	ENSMUST00000111377	Ensembl \| MGI Sequence Detail	3200	Not Applicable
polypeptide	ENSMUSP00000107008	Ensembl \| MGI Sequence Detail	382	Not Applicable

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UniProt

2 Sequences
Protein Ontology

PR:000009870 LIM homeobox transcription factor 1-alpha

(term hierarchy)
InterPro Domains

IPR017970 Homeobox, conserved site

IPR001356 Homeodomain

IPR009057 Homeodomain-like superfamily

IPR050453 LIM/homeobox transcription factors

IPR042688 Lmx1a, first LIM domain

IPR001781 Zinc finger, LIM-type

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All nucleic 46

Genomic 3

cDNA 21

Primer pair 7

Other 15

Antibodies 14

Microarray probesets 2

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MGD-MRK-14613, MGD-MRK-8891, MGI:94923

Summaries

All 269

Developmental Gene Expression 192

Diseases 1

Gene Ontology 14

Phenotypes 68
Earliest

J:15346 FALCONER DS, et al., [Dreher, a new gene of the waltzer-shaker group in the house mouse.]. Z Indukt Abstamm Vererbungsl. 1951;84(2):71-3
Latest

J:385405 Hermant C, et al., TBP regulates transposable element expression in early mouse embryos. EMBO J. 2026 May;45(9):3073-3101

TSS for Lmx1a:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr9906	Chr1:167516189-167516202 (+)	-610 bp
Tssr9907	Chr1:167516677-167516695 (+)	-120 bp
Tssr9908	Chr1:167516771-167516786 (+)	-27 bp
Tssr9909	Chr1:167517094-167517103 (+)	293 bp
Tssr9910	Chr1:167517121-167517132 (+)	321 bp
Tssr9911	Chr1:167517203-167517231 (+)	411 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