LHX8

gene
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Also known as Lhx7

Summary

LHX8 (LIM homeobox 8, HGNC:28838) is a protein-coding gene on chromosome 1p31.1, encoding LIM/homeobox protein Lhx8 (Q68G74). Transcription factor involved in differentiation of certain neurons and mesenchymal cells.

The protein encoded by this gene is a member of the LIM homeobox family of proteins, which are involved in patterning and differentiation of various tissue types. These proteins contain two tandemly repeated cysteine-rich double-zinc finger motifs known as LIM domains, in addition to a DNA-binding homeodomain. This family member is a transcription factor that plays a role in tooth morphogenesis. It is also involved in oogenesis and in neuronal differentiation. This gene is a candidate gene for cleft palate, and it is also associated with odontoma formation. Alternative splicing of this gene results in multiple transcript variants.

Source: NCBI Gene 431707 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): inherited primary ovarian failure (Limited, GenCC)
  • Clinical variants (ClinVar): 53 total
  • Transcription factor: yes — 12 downstream targets (CollecTRI)
  • MANE Select transcript: NM_001256114

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28838
Approved symbolLHX8
NameLIM homeobox 8
Location1p31.1
Locus typegene with protein product
StatusApproved
AliasesLhx7
Ensembl geneENSG00000162624
Ensembl biotypeprotein_coding
OMIM604425
Entrez431707

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 retained_intron

ENST00000294638, ENST00000356261, ENST00000607240, ENST00000696555, ENST00000929120, ENST00000929121

RefSeq mRNA: 2 — MANE Select: NM_001256114 NM_001001933, NM_001256114

CCDS: CCDS30756, CCDS58008

Canonical transcript exons

ENST00000356261 — 9 exons

ExonStartEnd
ENSE000013747297516081975161533
ENSE000016040177514858775148682
ENSE000016139747514384575143948
ENSE000017413727515689375157076
ENSE000017565057514311875143338
ENSE000034686367513660375136689
ENSE000036016747513710075137261
ENSE000036233277514098575141106
ENSE000039676897513438875134954

Expression profiles

Bgee: expression breadth broad, 66 present calls, max score 96.56.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3290 / max 39.3260, expressed in 98 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
35270.163460
35260.050722
35290.035018
35300.030911
35310.028617
35280.02048

Top tissues by expression

228 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065596.56gold quality
oocyteCL:000002395.06gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047381.75gold quality
buccal mucosa cellCL:000233679.86gold quality
oral cavityUBERON:000016772.60gold quality
minor salivary glandUBERON:000183071.49gold quality
mouth mucosaUBERON:000372969.70gold quality
saliva-secreting glandUBERON:000104465.99gold quality
caudate nucleusUBERON:000187361.59gold quality
putamenUBERON:000187460.78gold quality
lateral globus pallidusUBERON:000247658.29gold quality
lower lobe of lungUBERON:000894957.60silver quality
gall bladderUBERON:000211056.70gold quality
nucleus accumbensUBERON:000188256.51gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099154.14gold quality
tonsilUBERON:000237253.54gold quality
epithelium of nasopharynxUBERON:000195153.45gold quality
pharyngeal mucosaUBERON:000035551.84gold quality
gingivaUBERON:000182849.35silver quality
urinary bladderUBERON:000125549.24gold quality
globus pallidusUBERON:000187546.33silver quality
mucosa of paranasal sinusUBERON:000503045.23silver quality
esophagus mucosaUBERON:000246945.20gold quality
medial globus pallidusUBERON:000247744.85silver quality
middle temporal gyrusUBERON:000277144.77gold quality
testisUBERON:000047344.34gold quality
penisUBERON:000098943.84silver quality
left lobe of thyroid glandUBERON:000112043.79gold quality
thyroid glandUBERON:000204643.61gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451143.37gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-GEOD-93593yes1411.28
E-MTAB-8894yes491.19
E-ANND-3no2.91

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

12 targets.

TargetRegulation
AKT1
BDNF
BMP4Activation
BRAF
DUSP1
GSCActivation
IL2RA
LHX6Activation
MSX1Activation
MSX2Activation
PKLR
SCNN1A

Upstream regulators (CollecTRI, top): CREB1, JUN, JUNB, JUND, SOHLH1

miRNA regulators (miRDB)

120 targeting LHX8, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-3646100.0073.565283
HSA-MIR-5692A100.0074.406850
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-340-5P100.0072.504437
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-366299.9973.825684
HSA-MIR-480399.9871.993117
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-998599.9872.112939
HSA-MIR-548N99.9871.944170
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-50799.9770.111915
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-302E99.9670.742669
HSA-MIR-55799.9670.011640

Literature-anchored findings (GeneRIF, showing 10)

  • Sohlh1 and Lhx8 are two germ cell-specific, critical regulators of oogenesis (PMID:16690745)
  • Mutations in the LHX8 exons are uncommon in Caucasian women with premature ovarian failure. (PMID:17624344)
  • LHX8 might play an important role in odontoma formation. This is 1st report on comparison of LHX8 expression between human odontoma-derived mesenchymal cells and normal adult dental mesenchymal stem cells and its overexpression in human samples. (PMID:21143530)
  • Our tagging-single nucleotide polymorphism (tSNP)-based association analysis was negative for Tourette syndrome association with LHX8. (PMID:22435649)
  • Increasing Lhx8 expression in neuronal cell lines also increased acetylcholine release. (PMID:24316404)
  • Posttreatment monitoring by ASCL1/LHX8 methylation analysis in women with HIV treated for cervical intraepithelial neoplasia grade 2/3. (PMID:35152224)
  • Heterozygous loss-of-function variants in LHX8 cause female infertility characterized by oocyte maturation arrest. (PMID:36029299)
  • Validation of ASCL1 and LHX8 Methylation Analysis as Primary Cervical Cancer Screening Strategy in South African Women with Human Immunodeficiency Virus. (PMID:36366827)
  • Single-cell profiling of lncRNAs in human germ cells and molecular analysis reveals transcriptional regulation of LNC1845 on LHX8. (PMID:36602025)
  • LIM homeobox 8 reduced apoptosis and promoted periodontal tissue regeneration function of dental pulp stem cells. (PMID:38703583)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriolhx8aENSDARG00000002330
danio_reriolhx8bENSDARG00000042145
mus_musculusLhx8ENSMUSG00000096225
rattus_norvegicusLhx8ENSRNOG00000028348

Paralogs (20): FHL1 (ENSG00000022267), LMO3 (ENSG00000048540), LHX5 (ENSG00000089116), ZFHX4 (ENSG00000091656), LHX2 (ENSG00000106689), LHX6 (ENSG00000106852), LHX3 (ENSG00000107187), LHX4 (ENSG00000121454), LMO2 (ENSG00000135363), ZFHX2 (ENSG00000136367), LMX1B (ENSG00000136944), ZFHX3 (ENSG00000140836), LMO4 (ENSG00000143013), LHX9 (ENSG00000143355), CRIP3 (ENSG00000146215), LMX1A (ENSG00000162761), LMO1 (ENSG00000166407), CRIP2 (ENSG00000182809), CRIP1 (ENSG00000213145), LHX1 (ENSG00000273706)

Protein

Protein identifiers

LIM/homeobox protein Lhx8Q68G74 (reviewed: Q68G74)

All UniProt accessions (2): Q68G74, A0A8Q3WLD2

UniProt curated annotations — full annotation on UniProt →

Function. Transcription factor involved in differentiation of certain neurons and mesenchymal cells.

Subcellular location. Nucleus.

Isoforms (2)

UniProt IDNamesCanonical?
Q68G74-11yes
Q68G74-22

RefSeq proteins (2): NP_001001933, NP_001243043* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001356HDDomain
IPR001781Znf_LIMDomain
IPR009057Homeodomain-like_sfHomologous_superfamily
IPR017970Homeobox_CSConserved_site
IPR050453LIM_Homeobox_TFFamily

Pfam: PF00046, PF00412

UniProt features (8 total): domain 2, chain 1, DNA-binding region 1, region of interest 1, compositionally biased region 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q68G74-F169.460.38

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 110 (showing top): GOBP_FOREBRAIN_NEURON_DEVELOPMENT, GOBP_RESPONSE_TO_ETHANOL, BENPORATH_ES_WITH_H3K27ME3, GOBP_NEUROGENESIS, TACAATC_MIR508, GOBP_FOREBRAIN_DEVELOPMENT, GOBP_FOREBRAIN_GENERATION_OF_NEURONS, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1, GOBP_CENTRAL_NERVOUS_SYSTEM_NEURON_DIFFERENTIATION, GOBP_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, GOBP_HEAD_DEVELOPMENT, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, ACTTTAT_MIR1425P, GOBP_CENTRAL_NERVOUS_SYSTEM_NEURON_DEVELOPMENT, GOBP_RESPONSE_TO_ALCOHOL

GO Biological Process (5): regulation of transcription by RNA polymerase II (GO:0006357), forebrain neuron development (GO:0021884), neuron differentiation (GO:0030182), response to ethanol (GO:0045471), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (7): RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), metal ion binding (GO:0046872), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515), sequence-specific DNA binding (GO:0043565)

GO Cellular Component (2): chromatin (GO:0000785), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of DNA-templated transcription1
transcription by RNA polymerase II1
forebrain neuron differentiation1
central nervous system neuron development1
cell differentiation1
generation of neurons1
response to alcohol1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
transcription cis-regulatory region binding1
chromatin1
RNA polymerase II transcription regulatory region sequence-specific DNA binding1
DNA-binding transcription factor activity1
regulation of transcription by RNA polymerase II1
cation binding1
double-stranded DNA binding1
sequence-specific DNA binding1
nucleic acid binding1
binding1
DNA binding1
chromosome1
cellular anatomical structure1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

1530 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LHX8SOHLH1Q5JUK2962
LHX8NOBOXO60393928
LHX8FIGLAQ6QHK4918
LHX8GBX1Q14549897
LHX8MSX1P28360848
LHX8YBX2Q9Y2T7845
LHX8PAX9P55771795
LHX8SATB2Q9UPW6686
LHX8SOHLH2Q9NX45682
LHX8DLX2Q07687679
LHX8ZIC1Q15915671
LHX8HOXC9P31274664
LHX8HOXA2O43364647
LHX8NKX2-1P43699647
LHX8TMEM26Q6ZUK4629

IntAct

152 interactions, top by confidence:

ABTypeScore
LHX8FIGLApsi-mi:“MI:0915”(physical association)0.700
PYGO1BCL9psi-mi:“MI:0914”(association)0.700
LDB1LHX8psi-mi:“MI:0915”(physical association)0.690
LHX8LDB1psi-mi:“MI:0915”(physical association)0.690
LHX8LDB1psi-mi:“MI:0914”(association)0.690
KLF3LHX8psi-mi:“MI:0915”(physical association)0.560
LHX8NUTM1psi-mi:“MI:0915”(physical association)0.560
LHX8SCYL3psi-mi:“MI:0915”(physical association)0.560
LHX8KLF3psi-mi:“MI:0915”(physical association)0.560
NUTM1LHX8psi-mi:“MI:0915”(physical association)0.560
AXIN1LHX8psi-mi:“MI:0915”(physical association)0.560
EFSLHX8psi-mi:“MI:0915”(physical association)0.560
LHX8LDB1psi-mi:“MI:0915”(physical association)0.560
ZBTB24LHX8psi-mi:“MI:0915”(physical association)0.560
LDB2LHX8psi-mi:“MI:0915”(physical association)0.560
LHX8ATF6Bpsi-mi:“MI:0915”(physical association)0.560
FOXN1LHX8psi-mi:“MI:0915”(physical association)0.560
CSNK2A1LHX8psi-mi:“MI:0915”(physical association)0.560
LHX8TBC1D1psi-mi:“MI:0915”(physical association)0.560
LHX8GINS4psi-mi:“MI:0915”(physical association)0.560
NEDD9LHX8psi-mi:“MI:0915”(physical association)0.560

BioGRID (59): LHX8 (Two-hybrid), LHX8 (Two-hybrid), LHX8 (Two-hybrid), LHX8 (Two-hybrid), LHX8 (Affinity Capture-MS), LHX8 (Two-hybrid), LHX8 (Two-hybrid), LHX8 (Affinity Capture-MS), LHX8 (Two-hybrid), LHX8 (Two-hybrid), LHX8 (Two-hybrid), LHX8 (Two-hybrid), LHX8 (Two-hybrid), LHX8 (Two-hybrid), LHX8 (Two-hybrid)

ESM2 similar proteins: A0A8I6G705, A6QNT8, B5DFF2, D4A055, O00305, O14639, O16011, O19048, O95319, O95486, P56223, P60335, P60762, Q08DJ0, Q12800, Q13330, Q15365, Q15853, Q16514, Q3T174, Q4V860, Q5E9A3, Q5R8Y8, Q62599, Q63665, Q64705, Q68G74, Q6DH13, Q6NZH6, Q6P0B1, Q6ZRY4, Q792H5, Q7T2T1, Q7T2U9, Q86SE5, Q8K4B0, Q8K4G5, Q8K4Q0, Q8N122, Q8R0S4

Diamond homologs: A0JNI8, A2I8Z7, A2PZF9, G5EC36, G5EE86, O14639, O35652, O60663, O88609, O94929, O97581, P20154, P25791, P25800, P25801, P29673, P29674, P34764, P34765, P36198, P36200, P37137, P48742, P50211, P50212, P50458, P50480, P50481, P52889, P53405, P53406, P53407, P53408, P53409, P53410, P53411, P53412, P53413, P53667, P53668

SIGNOR signaling

1 interactions.

AEffectBMechanism
SOHLH1“up-regulates quantity by expression”LHX8“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

53 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance44
Likely benign6
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

1950 predictions. Top by Δscore:

VariantEffectΔscore
1:75140980:CACAG:Cacceptor_loss1.0000
1:75140983:A:AGacceptor_gain1.0000
1:75140984:G:GAacceptor_loss1.0000
1:75140984:G:GGacceptor_gain1.0000
1:75140984:GGT:Gacceptor_gain1.0000
1:75141104:CAGGT:Cdonor_loss1.0000
1:75141105:AGGT:Adonor_loss1.0000
1:75141106:GGTA:Gdonor_loss1.0000
1:75141107:G:GAdonor_loss1.0000
1:75141108:T:Gdonor_loss1.0000
1:75143326:G:GTdonor_gain1.0000
1:75143843:AG:Aacceptor_gain1.0000
1:75143843:AGG:Aacceptor_gain1.0000
1:75143844:GG:Gacceptor_gain1.0000
1:75143844:GGG:Gacceptor_gain1.0000
1:75143844:GGGA:Gacceptor_gain1.0000
1:75143844:GGGAA:Gacceptor_gain1.0000
1:75143947:AGGT:Adonor_loss1.0000
1:75143949:G:GGdonor_gain1.0000
1:75143950:T:Gdonor_loss1.0000
1:75157072:GGATG:Gdonor_gain1.0000
1:75157073:GATG:Gdonor_gain1.0000
1:75157073:GATGG:Gdonor_gain1.0000
1:75157075:TGG:Tdonor_loss1.0000
1:75157076:GGTA:Gdonor_loss1.0000
1:75157077:G:GGdonor_gain1.0000
1:75157077:GTA:Gdonor_loss1.0000
1:75157078:T:Adonor_loss1.0000
1:75140981:A:AGacceptor_gain0.9900
1:75140983:AG:Aacceptor_gain0.9900

AlphaMissense

2255 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:75137227:G:AC78Y1.000
1:75137254:T:CL87P1.000
1:75137257:T:CL88P1.000
1:75141000:T:AW95R1.000
1:75141000:T:CW95R1.000
1:75141005:T:AH96Q1.000
1:75141005:T:GH96Q1.000
1:75141012:T:AC99S1.000
1:75141012:T:CC99R1.000
1:75141013:G:CC99S1.000
1:75141014:T:GC99W1.000
1:75141016:T:AL100H1.000
1:75141016:T:CL100P1.000
1:75141021:T:AC102S1.000
1:75141021:T:CC102R1.000
1:75141022:G:AC102Y1.000
1:75141022:G:CC102S1.000
1:75141022:G:TC102F1.000
1:75141023:C:GC102W1.000
1:75141030:T:AC105S1.000
1:75141030:T:CC105R1.000
1:75141031:G:AC105Y1.000
1:75141031:G:CC105S1.000
1:75141031:G:TC105F1.000
1:75141032:C:GC105W1.000
1:75141060:T:CC115R1.000
1:75141061:G:AC115Y1.000
1:75141062:T:GC115W1.000
1:75141063:T:GY116D1.000
1:75141087:T:AC124S1.000

dbSNP variants (sampled 300 via entrez): RS1000027947 (1:75145546 A>C,T), RS1000178763 (1:75138678 A>G), RS1000191102 (1:75129771 G>T), RS1000193912 (1:75182625 G>A,T), RS1000251056 (1:75138345 T>C), RS1000340813 (1:75146957 TCAA>T), RS1000372764 (1:75158481 G>A), RS1000373437 (1:75147194 G>A), RS1000381539 (1:75177581 C>A,T), RS1000428104 (1:75132657 C>G), RS1000440639 (1:75193863 T>G), RS1000443065 (1:75145133 G>A), RS1000475003 (1:75177410 C>T), RS1000506609 (1:75154098 T>C), RS1000558234 (1:75195024 A>C,G)

Disease associations

OMIM: gene MIM:604425 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
inherited primary ovarian failureLimitedAutosomal dominant

Mondo (1): inherited primary ovarian failure (MONDO:0019852)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression5
trichostatin Aincreases expression, affects cotreatment3
entinostatincreases expression, affects cotreatment2
belinostatincreases expression, affects cotreatment2
Panobinostataffects cotreatment, increases expression2
Arsenicaffects methylation, increases methylation2
Cyclosporineincreases expression, decreases methylation2
p-Chloromercuribenzoic Acidaffects cotreatment, increases expression2
propionaldehydedecreases expression1
arseniteincreases methylation1
butyraldehydedecreases expression1
mercuric bromideaffects cotreatment, increases expression1
pentanaldecreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
jinfukangaffects cotreatment, decreases expression1
Sunitinibincreases expression1
Air Pollutantsdecreases expression1
Aldehydesdecreases expression1
Benzo(a)pyreneaffects methylation1
Cisplatinaffects cotreatment, decreases expression1
Tretinoinincreases expression1
Triclosandecreases expression1
Aflatoxin B1affects expression1
Asbestos, Serpentinedecreases methylation1
Asbestos, Crocidolitedecreases methylation1
Asbestos, Amositedecreases methylation1
Okadaic Aciddecreases expression1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_A3W5SEES3-1V human LHX8, clone1Embryonic stem cellMale
CVCL_A3W6SEES3-1V human LHX8, clone2Embryonic stem cellMale
CVCL_A3W7SEES3-1V human LHX8, clone3Embryonic stem cellMale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.