Article| Volume 25, ISSUE 7, 100839, July 2023

LHX2 haploinsufficiency causes a variable neurodevelopmental disorder

Published:April 10, 2023DOI:



      LHX2 encodes the LIM homeobox 2 transcription factor (LHX2), which is highly expressed in brain and well conserved across species, but it has not been clearly linked to neurodevelopmental disorders (NDDs) to date.


      Through international collaboration, we identified 19 individuals from 18 families with variable neurodevelopmental phenotypes, carrying a small chromosomal deletion, likely gene-disrupting or missense variants in LHX2. Functional consequences of missense variants were investigated in cellular systems.


      Affected individuals presented with developmental and/or behavioral abnormalities, autism spectrum disorder, variable intellectual disability, and microcephaly. We observed nucleolar accumulation for 2 missense variants located within the DNA-binding HOX domain, impaired interaction with co-factor LDB1 for another variant located in the protein-protein interaction–mediating LIM domain, and impaired transcriptional activation by luciferase assay for 4 missense variants.


      We implicate LHX2 haploinsufficiency by deletion and likely gene-disrupting variants as causative for a variable NDD. Our findings suggest a loss-of-function mechanism also for likely pathogenic LHX2 missense variants. Together, our observations underscore the importance of LHX2 in the nervous system and for variable neurodevelopmental phenotypes.


      To read this article in full you will need to make a payment

      Purchase one-time access:

      Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online access
      One-time access price info
      • For academic or personal research use, select 'Academic and Personal'
      • For corporate R&D use, select 'Corporate R&D Professionals'

      ACMG Member Login

      Are you an ACMG Member? Sign in for online access.


      Subscribe to Genetics in Medicine
      Already a print subscriber? Claim online access
      Already an online subscriber? Sign in
      Institutional Access: Sign in to ScienceDirect


        • Kochinke K.
        • Zweier C.
        • Nijhof B.
        • et al.
        Systematic phenomics analysis deconvolutes genes mutated in intellectual disability into biologically coherent modules.
        Am J Hum Genet. 2016; 98: 149-164
        • Xu Y.
        • Baldassare M.
        • Fisher P.
        • et al.
        LH-2: a LIM/homeodomain gene expressed in developing lymphocytes and neural cells.
        Proc Natl Acad Sci U S A. 1993; 90: 227-231
        • Hou P.S.
        • Chuang C.Y.
        • Kao C.F.
        • et al.
        LHX2 regulates the neural differentiation of human embryonic stem cells via transcriptional modulation of PAX6 and CER1.
        Nucleic Acids Res. 2013; 41: 7753-7770
        • Zibetti C.
        • Liu S.
        • Wan J.
        • Qian J.
        • Blackshaw S.
        Epigenomic profiling of retinal progenitors reveals LHX2 is required for developmental regulation of open chromatin.
        Commun Biol. 2019; 2: 142
        • Monahan K.
        • Horta A.
        • Lomvardas S.
        LHX2− and LDB1-mediated trans interactions regulate olfactory receptor choice.
        Nature. 2019; 565: 448-453
        • Rincón-Limas D.E.
        • Lu C.H.
        • Canal I.
        • et al.
        Conservation of the expression and function of apterous orthologs in Drosophila and mammals.
        Proc Natl Acad Sci U S A. 1999; 96: 2165-2170
        • Dawid I.B.
        • Toyama R.
        • Taira M.
        LIM domain proteins.
        C R Acad Sci III. 1995; 318: 295-306
        • Kinare V.
        • Iyer A.
        • Padmanabhan H.
        • et al.
        An evolutionarily conserved Lhx2-Ldb1 interaction regulates the acquisition of hippocampal cell fate and regional identity.
        Development. 2020; 147dev187856
        • Rincón-Limas D.E.
        • Lu C.H.
        • Canal I.
        • Botas J.
        The level of DLDB/CHIP controls the activity of the LIM homeodomain protein apterous: evidence for a functional tetramer complex in vivo.
        EMBO J. 2000; 19: 2602-2614
        • Porter F.D.
        • Drago J.
        • Xu Y.
        • et al.
        Lhx2, a LIM homeobox gene, is required for eye, forebrain, and definitive erythrocyte development.
        Development. 1997; 124: 2935-2944
        • Folgueras A.R.
        • Guo X.
        • Pasolli H.A.
        • et al.
        Architectural niche organization by LHX2 is linked to hair follicle stem cell function.
        Cell Stem Cell. 2013; 13: 314-327
        • Wandzioch E.
        • Kolterud A.
        • Jacobsson M.
        • Friedman S.L.
        • Carlsson L.
        Lhx2−/− mice develop liver fibrosis.
        Proc Natl Acad Sci U S A. 2004; 101: 16549-16554
        • Mangale V.S.
        • Hirokawa K.E.
        • Satyaki P.R.
        • et al.
        Lhx2 selector activity specifies cortical identity and suppresses hippocampal organizer fate.
        Science. 2008; 319: 304-309
        • Shu T.
        • Richards L.J.
        Cortical axon guidance by the glial wedge during the development of the corpus callosum.
        J Neurosci. 2001; 21: 2749-2758
        • Sobreira N.
        • Schiettecatte F.
        • Valle D.
        • Hamosh A.
        GeneMatcher: a matching tool for connecting investigators with an interest in the same gene.
        Hum Mutat. 2015; 36: 928-930
        • Gadd M.S.
        • Jacques D.A.
        • Nisevic I.
        • et al.
        A structural basis for the regulation of the LIM-homeodomain protein islet 1 (Isl1) by intra- and intermolecular interactions.
        J Biol Chem. 2013; 288: 21924-21935
        • Miyazono K.
        • Zhi Y.
        • Takamura Y.
        • et al.
        Cooperative DNA-binding and sequence-recognition mechanism of aristaless and clawless.
        EMBO J. 2010; 29: 1613-1623
        • Guex N.
        • Peitsch M.C.
        SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling.
        Electrophoresis. 1997; 18: 2714-2723
        • Sayle R.A.
        • Milner-White E.J.
        RASMOL: biomolecular graphics for all.
        Trends Biochem Sci. 1995; 20: 374
        • Thirunavukkarasu K.
        • Miles R.R.
        • Halladay D.L.
        • Onyia J.E.
        Cryptic enhancer elements in luciferase reporter vectors respond to the osteoblast-specific transcription factor Osf2/Cbfa1.
        BioTechniques. 2000; 28: 506-510
        • Kaplanis J.
        • Samocha K.E.
        • Wiel L.
        • et al.
        Evidence for 28 genetic disorders discovered by combining healthcare and research data.
        Nature. 2020; 586: 757-762
        • Richter F.
        • Morton S.U.
        • Kim S.W.
        • et al.
        Genomic analyses implicate noncoding de novo variants in congenital heart disease.
        Nat Genet. 2020; 52: 769-777
        • Zhou X.
        • Feliciano P.
        • Shu C.
        • et al.
        Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes.
        Nat Genet. 2022; 54: 1305-1319
        • Karczewski K.J.
        • Francioli L.C.
        • Tiao G.
        • et al.
        The mutational constraint spectrum quantified from variation in 141,456 humans.
        Nature. 2020; 581: 434-443
        • Lek M.
        • Karczewski K.J.
        • Minikel E.V.
        • et al.
        Analysis of protein-coding genetic variation in 60,706 humans.
        Nature. 2016; 536: 285-291
        • van Meyel D.J.
        • O’Keefe D.D.
        • Thor S.
        • Jurata L.W.
        • Gill G.N.
        • Thomas J.B.
        Chip is an essential cofactor for apterous in the regulation of axon guidance in Drosophila.
        Development. 2000; 127: 1823-1831
        • Chou S.J.
        • Tole S.
        Lhx2, an evolutionarily conserved, multifunctional regulator of forebrain development.
        Brain Res. 2019; 1705: 1-14
        • Chinn G.A.
        • Hirokawa K.E.
        • Chuang T.M.
        • et al.
        Agenesis of the corpus callosum due to defective glial wedge formation in Lhx2 mutant mice.
        Cereb Cortex. 2015; 25: 2707-2718
        • Godbole G.
        • Shetty A.S.
        • Roy A.
        • et al.
        Hierarchical genetic interactions between FOXG1 and LHX2 regulate the formation of the cortical hem in the developing telencephalon.
        Development. 2018; 145: dev154583
        • Konrad E.D.H.
        • Nardini N.
        • Caliebe A.
        • et al.
        CTCF variants in 39 individuals with a variable neurodevelopmental disorder broaden the mutational and clinical spectrum.
        Genet Med. 2019; 21: 2723-2733
        • Popp B.
        • Ekici A.B.
        • Thiel C.T.
        • et al.
        Exome Pool-Seq in neurodevelopmental disorders.
        Eur J Hum Genet. 2017; 25: 1364-1376
        • Posey J.E.
        • Rosenfeld J.A.
        • James R.A.
        • et al.
        Molecular diagnostic experience of whole-exome sequencing in adult patients.
        Genet Med. 2016; 18: 678-685
        • Karaca E.
        • Posey J.E.
        • Coban Akdemir Z.
        • et al.
        Phenotypic expansion illuminates multilocus pathogenic variation.
        Genet Med. 2018; 20: 1528-1537
        • Milán M.
        • Cohen S.M.
        Regulation of LIM homeodomain activity in vivo: a tetramer of dLDB and apterous confers activity and capacity for regulation by dLMO.
        Mol Cell. 1999; 4: 267-273
        • van Meyel D.J.
        • O’Keefe D.D.
        • Jurata L.W.
        • Thor S.
        • Gill G.N.
        • Thomas J.B.
        Chip and apterous physically interact to form a functional complex during Drosophila development.
        Mol Cell. 1999; 4: 259-265
        • Muralidharan B.
        • Khatri Z.
        • Maheshwari U.
        • et al.
        LHX2 interacts with the NuRD complex and regulates cortical neuron subtype determinants Fezf2 and Sox11.
        J Neurosci. 2017; 37: 194-203
        • Bendall A.J.
        • Rincón-Limas D.E.
        • Botas J.
        • Abate-Shen C.
        Protein complex formation between Msx1 and Lhx2 homeoproteins is incompatible with DNA binding activity.
        Differentiation. 1998; 63: 151-157
        • Audas T.E.
        • Jacob M.D.
        • Lee S.
        The nucleolar detention pathway: a cellular strategy for regulating molecular networks.
        Cell Cycle. 2012; 11: 2059-2062
        • Latonen L.
        Phase-to-phase with nucleoli – stress responses, protein aggregation and novel roles of RNA.
        Front Cell Neurosci. 2019; 13: 151