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Gene

LHX3

LIM homeobox 3

Summary

Cytogenetic location
9q34.3
Coordinates
Chromosome 9: 136,196,250–136,205,128 (GRCh38)
Exons
6 exons across 8.9 kb
Protein
397 amino acids
MANE Select transcript
ENST00000371748.10NM_178138.6
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • Hypogonadotropic Hypogonadism

    • Abnormal ovarian or testicular function due to insufficient hormonal stimulation from the hypothalamic-pituitary axis.

      • 4 GenCC submitters rate it definitive or strong

  • Non-Acquired Combined Pituitary Hormone Deficiency

    • Combined pituitary hormone deficiency, genetic form

      Inherited deficiency of several pituitary hormones, including PROP1, POU1F1, HESX1 and related causes.

      • 4 GenCC submitters rate it definitive or strong

    • Congenital hypopituitarism is characterized by multiple pituitary hormone deficiency, including somatotroph, thyrotroph, lactotroph, corticotroph or gonadotroph deficiencies, due to mutations of pituitary transcription factors involved in pituitary ontogenesis.

      • 4 GenCC submitters rate it definitive or strong

How LHX3 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 9, with a bracket where LHX3 sits. LHX3 and 20 genes near it on chromosome 9, from 135,700,689 to 136,700,688.Chromosome 99q34.3p24.3p24.2p24.1p23p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q13q21.11q21.12q21.13q21.2q21.31q21.32q21.33q22.1q22.2q22.31q22.32q22.33q31.1q31.2q31.3q32q33.1q33.2q33.3q34.11q34.12q34.13q34.2q34.3135.8 Mb136 Mb136.2 Mb136.4 Mb136.6 MbSOHLH1: 135,693,407–135,704,498, reverse strandSOHLH1KCNT1: 135,702,173–135,795,508, forward strandKCNT1CAMSAP1: 135,808,487–135,907,591, reverse strandCAMSAP1UBAC1: 135,924,661–135,961,400, reverse strandUBAC1NACC2: 136,006,537–136,095,327, reverse strandNACC2TMEM250: 136,113,067–136,118,946, reverse strandTMEM250LHX3: 136,196,250–136,205,128, reverse strandLHX3QSOX2: 136,206,332–136,245,831, reverse strandQSOX2CCDC187: 136,249,973–136,306,901, reverse strandCCDC187GPSM1: 136,327,425–136,359,608, forward strandGPSM1DNLZ: 136,359,480–136,363,773, reverse strandDNLZ: 136,361,904–136,373,644, reverse strandCARD9: 136,363,956–136,373,683, reverse strandCARD9SNAPC4: 136,375,567–136,400,226, reverse strandENTR1: 136,401,922–136,410,621, reverse strandENTR1PMPCA: 136,410,630–136,428,006, forward strandPMPCAINPP5E: 136,428,615–136,439,882, reverse strandINPP5ESEC16A: 136,440,096–136,483,843, reverse strandSEC16ANOTCH1: 136,494,433–136,546,048, reverse strandNOTCH1EGFL7: 136,658,284–136,672,684, forward strandEGFL7AGPAT2: 136,673,142–136,687,483, reverse strandAGPAT2Diagram of LHX3: 6 exons on the reverse strand of chromosome 9Exon 6: 5 known disease-causing sitesExon 5: 3 known disease-causing sitesExon 4: 3 known disease-causing sitesExon 3: 4 known disease-causing sitesExon 2: 6 known disease-causing sitesExon 6: 136,196,250–136,197,743, 1,494 basesExon 5: 136,198,652–136,198,820, 169 basesExon 4: 136,198,908–136,199,059, 152 basesExon 3: 136,199,678–136,199,880, 203 basesExon 2: 136,200,582–136,200,753, 172 basesExon 1: 136,204,934–136,205,128, 195 bases6543215′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 2.4 kb of the gene's 8.9 kb; 1,194 of those bases code for the protein.

How a genome test reads LHX3

25

positions in LHX3 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 8.9 kb of LHX3, introns included, not only the 2.4 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). LHX3 gene: LIM homeobox 3. Retrieved 17 October 2026, from https://dantelabs.com/genes/lhx3

Vancouver

Dante Labs. LHX3 gene: LIM homeobox 3 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/lhx3

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