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Lhx6 Gene Detail
Summary
  • Symbol
    Lhx6
  • Name
    LIM homeobox protein 6
  • Feature Type
    protein coding gene
  • IDs
    MGI:1306803
    NCBI Gene: 16874
  • Alliance
    genome feature page
  • Transcription Start Sites
    5 TSS
Location &
Maps
more
  • Sequence Map
    Chr2:35971965-35995420 bp, - strand
    From Ensembl annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 2, 24.17 cM
  • Mapping Data
    1 experiment
Strain
Comparison
more
  • SNPs within 2kb
    413 from dbSNP Build 142
  • Strain Annotations
    19
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_1306803
 protein coding gene Chr2:35971962-35996004 (-)
129S1/SvImJ ENSMUSG00200044344
 protein coding gene Chr2:32957447-32980914 (-)
A/J ENSMUSG00195036905
 protein coding gene Chr2:33059472-33082936 (-)
AKR/J ENSMUSG00220041978
 protein coding gene Chr2:33174490-33197957 (-)
BALB/cJ ENSMUSG00180045900
 protein coding gene Chr2:33073890-33097357 (-)
C3H/HeJ ENSMUSG00175038073
 protein coding gene Chr2:33040206-33063671 (-)
C57BL/6NJ ENSMUSG00215046334
 protein coding gene Chr2:33107340-33130803 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0023487
 protein coding gene Chr2:31970952-31994445 (-)
CAST/EiJ ENSTCUG00005016713
 protein coding gene Chr2:32759407-32782954 (-)
CBA/J ENSMUSG00210049597
 protein coding gene Chr2:33112486-33135949 (-)
DBA/2J ENSMUSG00185042966
 protein coding gene Chr2:32972294-32995763 (-)
FVB/NJ ENSMUSG00205026510
 protein coding gene Chr2:32824121-32847591 (-)
JF1/MsJ ENSUMUG00000008272
 protein coding gene Chr2:32865298-32888832 (-)
LP/J ENSMUSG00230045077
 protein coding gene Chr2:34892688-34916159 (-)
NOD/ShiLtJ ENSMUSG00190028079
 protein coding gene Chr2:33079031-33102496 (-)
NZO/HlLtJ ENSMUSG00225048682
 protein coding gene Chr2:42656147-42679612 (-)
PWK/PhJ ENSLUMG00010037586
 protein coding gene Chr2:32956230-32979688 (-)
SPRET/EiJ ENSMSPG00010040206
 protein coding gene Chr2:33660613-33684156 (-)
WSB/EiJ ENSIUOG00005039704
 protein coding gene Chr2:32959979-32983422 (-)



Homology
more
  • Human Ortholog
    LHX6, LIM homeobox 6
  • Vertebrate Orthologs
    4
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    LHX6, LIM homeobox 6
  • Synonyms
    hLHX6, LHX6.1
  • Links
    NCBI Gene ID: 26468
    UniProt: Q9UPM6

  • Chr Location
    9q33.2; chr9:122202577-122229626 (-)  GRCh38
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    20 phenotypes from 4 alleles in 4 genetic backgrounds
    3 phenotypes from multigenic genotypes
    38 phenotype references
Phenotype Overview

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.
Homozygous mutation of this gene results in impaired migration and specification of cortical interneurons, postnatal lethality and weakness.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    23
  • GO References
    9
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.
Expression
less
Expression Overview

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
    1417
  • Tissues
    432
  • cDNA Data
    25
  • Literature Summary
    225
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000026890 Ensembl Gene Model | MGI Sequence Detail 23456 C57BL/6J ±  kb
    transcript ENSMUST00000112960 Ensembl | MGI Sequence Detail 3345 Not Applicable  
    polypeptide ENSMUSP00000108584 Ensembl | MGI Sequence Detail 392 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 62
      cDNA 31
      Primer pair 7
      Other 24
      Antibodies 9

      Microarray probesets 4
    References
    more
    • Summaries
      All 289
      Developmental Gene Expression 225
      Gene Ontology 9
      Phenotypes 38
    • Earliest
      J:48134 Grigoriou M, et al., Expression and regulation of Lhx6 and Lhx7, a novel subfamily of LIM homeodomain encoding genes, suggests a role in mammalian head development. Development. 1998 Jun;125(11):2063-74
    • Latest
      J:383107 Molero AE, et al., Aberrant medial ganglionic eminence (MGE) GABAergic neurogenesis contributes to Huntington's disease pathogenesis. Neurobiol Dis. 2026 Apr;221:107297
    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)
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    Funding Information
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    Send questions and comments to User Support.     		last database update
    09/08/2026
    MGI 6.24     		The Jackson Laboratory