LHX1

Summary

LHX1 (LIM homeobox 1, HGNC:6593) is a protein-coding gene on chromosome 17q12, encoding LIM/homeobox protein Lhx1 (P48742). Potential transcription factor.

This gene encodes a member of a large protein family which contains the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein is a transcription factor important for the development of the renal and urogenital systems. This gene is a candidate for Mayer-Rokitansky-Kuster-Hauser syndrome, a disorder characterized by anomalies in the female genital tract.

Source: NCBI Gene 3975 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 57 total — 1 likely-pathogenic
• Phenotypes (HPO): 21
• MANE Select transcript: NM_005568

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:6593
Approved symbol	LHX1
Name	LIM homeobox 1
Location	17q12
Locus type	gene with protein product
Status	Approved
Aliases	LIM-1, LIM1
Ensembl gene	ENSG00000273706
Ensembl biotype	protein_coding
OMIM	601999
Entrez	3975

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 3 protein_coding, 2 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000614239, ENST00000616237, ENST00000619297, ENST00000619939, ENST00000621767, ENST00000673652, ENST00000899090

RefSeq mRNA: 1 — MANE Select: NM_005568 NM_005568

CCDS: CCDS11316

Canonical transcript exons

ENST00000614239 — 5 exons

Exon	Start	End
ENSE00003717684	36942200	36942365
ENSE00003718820	36940610	36940887
ENSE00003723980	36937475	36938367
ENSE00003725548	36940290	36940516
ENSE00003736249	36942752	36944612

Expression profiles

Bgee: expression breadth broad, 50 present calls, max score 91.98.

FANTOM5 (CAGE): breadth broad, TPM avg 1.6044 / max 166.8877, expressed in 355 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
160443	1.6044	355

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellum	UBERON:0002037	91.98	gold quality
cerebellar cortex	UBERON:0002129	91.95	gold quality
cerebellar hemisphere	UBERON:0002245	91.86	gold quality
right hemisphere of cerebellum	UBERON:0014890	90.95	gold quality
adult mammalian kidney	UBERON:0000082	82.81	gold quality
kidney	UBERON:0002113	79.44	gold quality
metanephros cortex	UBERON:0010533	79.43	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	72.97	gold quality
cortex of kidney	UBERON:0001225	66.71	gold quality
hypothalamus	UBERON:0001898	64.59	gold quality
right uterine tube	UBERON:0001302	59.15	gold quality
substantia nigra	UBERON:0002038	56.90	gold quality
ventricular zone	UBERON:0003053	56.20	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	54.44	gold quality
fallopian tube	UBERON:0003889	52.24	gold quality
colonic epithelium	UBERON:0000397	51.32	gold quality
sural nerve	UBERON:0015488	51.06	gold quality
brain	UBERON:0000955	46.63	gold quality
prefrontal cortex	UBERON:0000451	42.12	gold quality
bone marrow cell	CL:0002092	41.85	gold quality
left uterine tube	UBERON:0001303	41.53	gold quality
ganglionic eminence	UBERON:0004023	41.06	silver quality
frontal cortex	UBERON:0001870	40.66	gold quality
endocervix	UBERON:0000458	39.42	gold quality
right frontal lobe	UBERON:0002810	39.13	gold quality
Brodmann (1909) area 9	UBERON:0013540	38.79	gold quality
cerebral cortex	UBERON:0000956	38.72	gold quality
Ammon’s horn	UBERON:0001954	38.62	gold quality
blood	UBERON:0000178	37.99	silver quality
dorsolateral prefrontal cortex	UBERON:0009834	37.87	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-8894	yes	315.98
E-HCAD-5	yes	18.90
E-ANND-3	no	2.09

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

6 targets.

Target	Regulation
CHRD	Unknown
HESX1	Activation
HHEX
NPY	Unknown
PAX8
RELN	Unknown

JASPAR motifs

Motif	Name	Family
MA1518.1	LHX1	HD-LIM

JASPAR matrix evidence (PMIDs): PMID:18585359

Upstream regulators (CollecTRI, top): HNF1B, ISL1

miRNA regulators (miRDB)

114 targeting LHX1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-96-5P	99.95	72.80	2140
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-3143	99.93	71.96	3104

Literature-anchored findings (GeneRIF, showing 11)

• Lim1 (also known as Lhx1) gene consists of a DNA-binding homeodomain and 2 cysteine-rich LIM domains, which may participate in protein to protein interactions, and encodes a transcription factor. (PMID:19849868)
• findings establish that the developmental marker Lim1 acts as an oncogene in cancer cells and targeting Lim1 may constitute an innovative therapeutic intervention in human lear cell carcinoma (PMID:21132009)
• Eleven dysplastic kidneys showed no expression of LIM1. In contrast, 12 of 32 nephroblastomas showed nuclear positivity. (PMID:21778788)
• Mutations in the coding regions of LHX1 may not be a common genetic etiologic factor involved in Han Chinese patients with mullerian duct abnormalities. (PMID:22217964)
• Lim1/LIM1 expression in neonatal, adult mouse and human endometrium suggesting Lim1/LIM1 may have a role in endometrial development and remodelling (PMID:22231913)
• study concludes that heterozygous mutations of LHX1 might be one cause of the Mayer-Rokitansky-Kuster-Hauser syndrome in a subgroup of patients (PMID:22740494)
• Data indicate that expression of ERAS, LHX1, and CCRK is increased in aggressive subgroups of medulloblastomas. (PMID:22875024)
• Data have identified TBX6 as a new gene associated with Mullerian aplasia. The results also support the relevance of LHX1 and CNVs in the development of this congenital malformation. (PMID:23954021)
• Report novel missense mutation in LHX1 in congenital absence of the uterus and vagina which could change the transcriptional activity of LHX1 and its effect on the regulation of the downstream target gene GSC. (PMID:28061432)
• Our MRKH families included 43 quads, 26 trios, and 30 duos. Of our MRKH probands, 87/147 (59%) had MRKH type 1 and 60/147 (41%) had type 2 with additional anomalies. CONCLUSION(S): Although the prevalence of WNT4, HNF1B, and LHX1 point mutations is low in people with MRKH, the prevalence of CNVs was approximately 19%. (PMID:28600106)
• The potential pro-metastatic role of Lim1 in advanced clear cell renal cell carcinoma in vitro, ex vivo, and in vivo in a nude mouse model. Lim1 was found constitutively expressed in all metastatic tissues. Lim1 silencing decreased pulmonary metastasis in the in vivo model. Lim1 is involved in the expression of various proteins regulating cell movements and EMT, and induced clonogenicity in CCC cells. (PMID:30076415)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lhx1	ENSMUSG00000018698
rattus_norvegicus	Lhx1	ENSRNOG00000002812

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), LHX8 (ENSG00000162624), LMX1A (ENSG00000162761), LMO1 (ENSG00000166407), CRIP2 (ENSG00000182809), CRIP1 (ENSG00000213145)

Protein

Protein identifiers

LIM/homeobox protein Lhx1 — P48742 (reviewed: P48742)

Alternative names: Homeobox protein Lim-1

All UniProt accessions (2): P48742, A0A087WY40

UniProt curated annotations — full annotation on UniProt →

Function. Potential transcription factor. May play a role in early mesoderm formation and later in lateral mesoderm differentiation and neurogenesis.

Subunit / interactions. Interacts with LDB1 via the tandem LIM domains.

Subcellular location. Nucleus.

Tissue specificity. Expressed in the brain, thymus, and tonsils. Expressed in samples from patients with chronic myeloid leukemia (CML) and in 58% of acute myeloid leukemia (AML) cell lines.

Domain organisation. The LIM domains exert a negative regulatory function and disruption of the LIM domains produces an activated form. In addition, two activation domains and a negative regulatory domain exist C-terminally to the homeobox.

RefSeq proteins (1): NP_005559* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001356	HD	Domain
IPR001781	Znf_LIM	Domain
IPR009057	Homeodomain-like_sf	Homologous_superfamily
IPR017970	Homeobox_CS	Conserved_site
IPR049618	Lhx1/5_LIM1	Domain
IPR049619	Lhx1/5_LIM2	Domain
IPR050453	LIM_Homeobox_TF	Family

Pfam: PF00046, PF00412

UniProt features (14 total): compositionally biased region 4, sequence conflict 3, domain 2, region of interest 2, chain 1, modified residue 1, DNA-binding region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P48742-F1	67.62	0.39

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 162

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

ID	Pathway
R-HSA-9761174	Formation of intermediate mesoderm
R-HSA-9830364	Formation of the nephric duct
R-HSA-9831926	Nephron development
R-HSA-1266738	Developmental Biology
R-HSA-9758941	Gastrulation
R-HSA-9830369	Kidney development

MSigDB gene sets: 347 (showing top): GOBP_SPINAL_CORD_DEVELOPMENT, GOBP_POSITIVE_REGULATION_OF_EPITHELIAL_CELL_DIFFERENTIATION, AHRARNT_01, GOBP_MORPHOGENESIS_OF_AN_EPITHELIUM, GOBP_METANEPHRIC_NEPHRON_MORPHOGENESIS, GOBP_HINDBRAIN_DEVELOPMENT, RRAGTTGT_UNKNOWN, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_URETER_DEVELOPMENT, GOBP_METENCEPHALON_DEVELOPMENT, GOBP_AXIS_SPECIFICATION, WWTAAGGC_UNKNOWN, GOBP_REGULATION_OF_MORPHOGENESIS_OF_A_BRANCHING_STRUCTURE, GOBP_METANEPHROS_DEVELOPMENT

GO Biological Process (77): urogenital system development (GO:0001655), ureteric bud development (GO:0001657), branching involved in ureteric bud morphogenesis (GO:0001658), gastrulation with mouth forming second (GO:0001702), ectoderm formation (GO:0001705), endoderm formation (GO:0001706), kidney development (GO:0001822), regulation of transcription by RNA polymerase II (GO:0006357), transcription by RNA polymerase II (GO:0006366), cell-cell signaling (GO:0007267), pattern specification process (GO:0007389), nervous system development (GO:0007399), motor neuron axon guidance (GO:0008045), anatomical structure morphogenesis (GO:0009653), post-embryonic development (GO:0009791), embryonic pattern specification (GO:0009880), animal organ morphogenesis (GO:0009887), anterior/posterior axis specification (GO:0009948), anterior/posterior pattern specification (GO:0009952), dorsal/ventral pattern formation (GO:0009953), regulation of gene expression (GO:0010468), retina layer formation (GO:0010842), ventral spinal cord development (GO:0021517), spinal cord association neuron differentiation (GO:0021527), telencephalon development (GO:0021537), cerebellum development (GO:0021549), cerebellar Purkinje cell differentiation (GO:0021702), forebrain regionalization (GO:0021871), cerebellar Purkinje cell-granule cell precursor cell signaling (GO:0021937), neuron differentiation (GO:0030182), somite rostral/caudal axis specification (GO:0032525), metanephric part of ureteric bud development (GO:0035502), oviduct epithelium development (GO:0035846), uterine epithelium development (GO:0035847), nephric duct elongation (GO:0035849), positive regulation of embryonic development (GO:0040019), cellular response to fibroblast growth factor stimulus (GO:0044344), negative regulation of DNA-templated transcription (GO:0045892), positive regulation of DNA-templated transcription (GO:0045893), mesendoderm development (GO:0048382)

GO Molecular Function (10): RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), cis-regulatory region sequence-specific DNA binding (GO:0000987), DNA-binding transcription factor activity (GO:0003700), zinc ion binding (GO:0008270), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515), sequence-specific DNA binding (GO:0043565), metal ion binding (GO:0046872)

GO Cellular Component (4): chromatin (GO:0000785), nucleus (GO:0005634), transcription regulator complex (GO:0005667), protein-containing complex (GO:0032991)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Kidney development	2
Developmental Biology	2
Gastrulation	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transcription cis-regulatory region binding	3
system development	2
renal system development	2
formation of primary germ layer	2
animal organ development	2
regulation of DNA-templated transcription	2
multicellular organism development	2
multicellular organismal process	2
regionalization	2
mesonephric tubule development	1
branching morphogenesis of an epithelial tube	1
ureteric bud morphogenesis	1
gastrulation	1
ectoderm development	1
endoderm development	1
transcription by RNA polymerase II	1
DNA-templated transcription	1
cell communication	1
signaling	1
axon guidance	1
developmental process	1
anatomical structure development	1
pattern specification process	1
embryo development	1
anatomical structure morphogenesis	1
axis specification	1
anterior/posterior pattern specification	1
chromatin	1
RNA polymerase II transcription regulatory region sequence-specific DNA binding	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transcription regulator activity	1
transition metal ion binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
nucleic acid binding	1
binding	1
DNA binding	1
cation binding	1
chromosome	1

Protein interactions and networks

STRING

1746 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LHX1	LDB1	Q86U70	914
LHX1	LDB2	O43679	838
LHX1	NEUROG2	Q9H2A3	804
LHX1	PAX2	Q02962	756
LHX1	EVX1	P49640	746
LHX1	RAB2A	P08886	722
LHX1	NKX2-2	O95096	711
LHX1	SIX2	Q9NPC8	683
LHX1	NEUROG1	Q92886	677
LHX1	EOMES	O95936	672
LHX1	RLIM	Q9NVW2	647
LHX1	PAX8	Q06710	630
LHX1	ASCL1	P50553	630
LHX1	EMX2	Q04743	622
LHX1	BCL6B	Q8N143	616

IntAct

23 interactions, top by confidence:

A	B	Type	Score
SSBP3	LHX1	psi-mi:“MI:0914”(association)	0.570
LHX1	C2CD6	psi-mi:“MI:0915”(physical association)	0.560
LHX1	KANK2	psi-mi:“MI:0915”(physical association)	0.560
LHX1	SCNM1	psi-mi:“MI:0915”(physical association)	0.560
LHX1	LDB1	psi-mi:“MI:0915”(physical association)	0.560
SSBP4	GM2A	psi-mi:“MI:0914”(association)	0.530
LHX1	PABPC1	psi-mi:“MI:0915”(physical association)	0.400
	LHX1	psi-mi:“MI:0915”(physical association)	0.370
SSBP3	LHX1	psi-mi:“MI:0914”(association)	0.350
LHX1	AIFM1	psi-mi:“MI:0914”(association)	0.350
LHX1	ZNF724	psi-mi:“MI:2364”(proximity)	0.270
C2CD6	LHX1	psi-mi:“MI:0915”(physical association)	0.000
LDB1	LHX1	psi-mi:“MI:0915”(physical association)	0.000
KANK2	LHX1	psi-mi:“MI:0915”(physical association)	0.000
SCNM1	LHX1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (110): LHX1 (Affinity Capture-MS), LHX1 (Affinity Capture-MS), LHX1 (Affinity Capture-MS), LHX1 (Affinity Capture-MS), FOXA2 (Reconstituted Complex), LHX1 (Two-hybrid), LHX1 (Two-hybrid), LHX1 (Two-hybrid), LHX1 (Two-hybrid), LHX1 (Proximity Label-MS), LHX1 (Reconstituted Complex), LHX3 (Reconstituted Complex), LHX1 (Affinity Capture-RNA), LHX1 (Affinity Capture-MS), LHX1 (Affinity Capture-MS)

ESM2 similar proteins: A0JNI8, A2I8Z7, A2PZF9, G5EC36, G5EE86, G5EEA1, P20154, P29673, P29674, P34764, P34765, P36198, P36200, P37137, P48742, P50211, P50212, P50458, P50481, P52889, P53405, P53406, P53407, P53408, P53409, P53411, P53412, P61371, P61372, P61373, P61374, P61375, P61376, P63006, P63007, P63008, Q1LWV4, Q5IS44, Q5IS89, Q68EY3

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.

A	Effect	B	Mechanism
LHX1	“up-regulates activity”	OTX2	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	42
Likely benign	9
Benign	4

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
997067	GRCh37/hg19 17q12(chr17:34841190-35733119)	Likely pathogenic

SpliceAI

795 predictions. Top by Δscore:

Variant	Effect	Δscore
17:36940474:C:CG	donor_gain	1.0000
17:36940474:C:G	donor_gain	1.0000
17:36940515:GG:G	donor_gain	1.0000
17:36940515:GGGT:G	donor_loss	1.0000
17:36940516:GG:G	donor_gain	1.0000
17:36940517:G:GA	donor_loss	1.0000
17:36940608:A:AG	acceptor_gain	1.0000
17:36940609:G:GG	acceptor_gain	1.0000
17:36940609:GCCA:G	acceptor_gain	1.0000
17:36942364:AG:A	donor_loss	1.0000
17:36942365:GG:G	donor_loss	1.0000
17:36938365:CCGG:C	donor_loss	0.9900
17:36938366:CGGTG:C	donor_loss	0.9900
17:36938367:GGT:G	donor_loss	0.9900
17:36938368:G:GG	donor_gain	0.9900
17:36938368:GTGA:G	donor_loss	0.9900
17:36938369:TGAG:T	donor_loss	0.9900
17:36938370:GAG:G	donor_loss	0.9900
17:36940289:GGT:G	acceptor_gain	0.9900
17:36940478:G:GG	donor_gain	0.9900
17:36940517:G:GG	donor_gain	0.9900
17:36940518:T:G	donor_loss	0.9900
17:36940605:CTTA:C	acceptor_loss	0.9900
17:36940606:TTA:T	acceptor_loss	0.9900
17:36940609:G:A	acceptor_loss	0.9900
17:36940609:GC:G	acceptor_gain	0.9900
17:36940609:GCC:G	acceptor_gain	0.9900
17:36940609:GCCAC:G	acceptor_gain	0.9900
17:36940883:TTCAG:T	donor_loss	0.9900
17:36940884:TCAG:T	donor_loss	0.9900

AlphaMissense

2676 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:36938207:T:A	C4S	1.000
17:36938207:T:C	C4R	1.000
17:36938208:G:A	C4Y	1.000
17:36938208:G:C	C4S	1.000
17:36938209:T:G	C4W	1.000
17:36938216:T:A	C7S	1.000
17:36938216:T:C	C7R	1.000
17:36938217:G:A	C7Y	1.000
17:36938217:G:C	C7S	1.000
17:36938218:C:G	C7W	1.000
17:36938229:T:A	I11N	1.000
17:36938229:T:C	I11T	1.000
17:36938240:T:C	F15L	1.000
17:36938242:T:A	F15L	1.000
17:36938242:T:G	F15L	1.000
17:36938244:T:C	L16P	1.000
17:36938267:T:A	W24R	1.000
17:36938267:T:C	W24R	1.000
17:36938269:G:C	W24C	1.000
17:36938269:G:T	W24C	1.000
17:36938271:A:G	H25R	1.000
17:36938272:C:A	H25Q	1.000
17:36938272:C:G	H25Q	1.000
17:36938279:T:A	C28S	1.000
17:36938279:T:C	C28R	1.000
17:36938280:G:A	C28Y	1.000
17:36938280:G:C	C28S	1.000
17:36938280:G:T	C28F	1.000
17:36938281:C:G	C28W	1.000
17:36938283:T:A	V29D	1.000

dbSNP variants (sampled 300 via entrez): RS1000296484 (17:36941031 C>A,T), RS1000875830 (17:36938833 TAG>T), RS1000924412 (17:36935304 C>T), RS1001296353 (17:36939606 G>C), RS1001349723 (17:36939353 T>C), RS1001727182 (17:36943378 C>T), RS1002186940 (17:36944297 A>T), RS1002349488 (17:36937937 G>A,C), RS1002885508 (17:36936173 CA>C), RS1003302052 (17:36937125 G>A,T), RS1003354473 (17:36936657 C>G), RS1003452956 (17:36942944 A>G), RS1003579277 (17:36942635 C>G,T), RS1003727155 (17:36941154 C>A), RS1004248765 (17:36944733 G>C)

Disease associations

OMIM: gene MIM:601999 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

21 total (21 of 21 shown, HPO-id order):

HPO	Term
HP:0000003	Multicystic kidney dysplasia
HP:0000028	Cryptorchidism
HP:0000049	Shawl scrotum
HP:0000070	Ureterocele
HP:0000083	Renal insufficiency
HP:0000239	Large fontanelles
HP:0000365	Hearing impairment
HP:0000717	Autism
HP:0000819	Diabetes mellitus
HP:0001249	Intellectual disability
HP:0001250	Seizure
HP:0001263	Global developmental delay
HP:0001562	Oligohydramnios
HP:0002059	Cerebral atrophy
HP:0002463	Language impairment
HP:0002910	Elevated circulating hepatic transaminase concentration
HP:0004322	Short stature
HP:0008678	Renal hypoplasia/aplasia
HP:0011968	Feeding difficulties
HP:0012157	Subcortical cerebral atrophy
HP:0100801	Pancreatic aplasia

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST005951_15	Body mass index	3.000000e-13
GCST007281_2	HDL cholesterol x physical activity interaction (1df test)	3.000000e-08
GCST007282_14	HDL cholesterol x physical activity interaction (2df test)	7.000000e-07
GCST007600_85	Alzheimer’s disease	3.000000e-06
GCST010151_27	Carotid intima media thickness x smoking interaction	4.000000e-06
GCST011011_38	Youthful appearance (self-reported)	1.000000e-08

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index
EFO:0003940	physical activity
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0007805	HDL cholesterol change measurement
EFO:0006527	smoking status measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression	3
Benzo(a)pyrene	affects methylation, increases methylation	2
Tretinoin	affects expression, increases expression	2
Particulate Matter	increases abundance, increases expression, affects expression	2
sotorasib	affects cotreatment, decreases expression	1
methylmercuric chloride	increases expression	1
titanium dioxide	increases methylation	1
terbufos	increases methylation	1
arsenite	increases methylation	1
ferrous chloride	decreases expression	1
abrine	decreases expression	1
trametinib	affects cotreatment, decreases expression	1
NVP-BKM120	affects cotreatment, decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Calcitriol	increases expression	1
Dust	decreases expression	1
Fonofos	increases methylation	1
Fluorouracil	decreases expression	1
Indomethacin	decreases expression	1
Parathion	increases methylation	1
Silicon Dioxide	increases methylation	1
Aflatoxin B1	increases methylation	1
Sodium Selenite	increases expression	1
S-Nitrosoglutathione	increases expression	1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

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

Cellosaurus	Name	Category	Sex
CVCL_A3U7	SEES3-1V human LHX1, clone1	Embryonic stem cell	Male
CVCL_A3U8	SEES3-1V human LHX1, clone2	Embryonic stem cell	Male
CVCL_A3U9	SEES3-1V human LHX1, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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