LHX1

LIM homeobox 1, the group of LIM class homeoboxes

Basic information

Region (hg38): 17:36936785-36944612

Links

ENSG00000273706 ∙ NCBI:3975 ∙ OMIM:601999 ∙ HGNC:6593 ∙ Uniprot:P48742 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LHX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LHX1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5	2	7
missense			14	1	1	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding						0
Total	0	0	14	6	3

Variants in LHX1

This is a list of pathogenic ClinVar variants found in the LHX1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-36938294-G-C		Inborn genetic diseases	Uncertain significance (May 31, 2023)
17-36938366-C-A		LHX1-related disorder	Benign (Sep 25, 2019)
17-36940278-AC-A		LHX1-related disorder	Likely benign (Jul 25, 2019)
17-36940290-G-A		Inborn genetic diseases	Likely benign (Jul 19, 2023)
17-36940360-A-G		Inborn genetic diseases	Uncertain significance (Apr 08, 2024)
17-36940511-A-C		Inborn genetic diseases	Uncertain significance (Jun 26, 2023)
17-36940617-G-A		LHX1-related disorder	Benign (Feb 21, 2019)
17-36940628-C-A		LHX1-related disorder	Benign (Jan 07, 2020)
17-36940732-C-A		Inborn genetic diseases	Uncertain significance (Oct 26, 2022)
17-36940736-A-G		Inborn genetic diseases	Uncertain significance (May 25, 2022)
17-36940744-G-A		Inborn genetic diseases	Uncertain significance (Nov 29, 2023)
17-36940833-C-T		LHX1-related disorder	Likely benign (Oct 28, 2019)
17-36942785-A-G		Inborn genetic diseases	Uncertain significance (Jan 03, 2024)
17-36942812-C-A		Inborn genetic diseases	Uncertain significance (Mar 06, 2023)
17-36942830-C-T		Inborn genetic diseases	Uncertain significance (Feb 23, 2023)
17-36942859-T-A		Inborn genetic diseases	Uncertain significance (Feb 10, 2022)
17-36942878-C-T		Inborn genetic diseases	Uncertain significance (Oct 05, 2023)
17-36942913-C-A		Inborn genetic diseases	Uncertain significance (Apr 29, 2024)
17-36942929-C-T		Inborn genetic diseases	Uncertain significance (Dec 22, 2023)
17-36942930-G-A		LHX1-related disorder	Likely benign (May 02, 2019)
17-36942961-C-G		Inborn genetic diseases	Uncertain significance (Dec 09, 2023)
17-36943007-A-G		Inborn genetic diseases	Uncertain significance (Nov 22, 2022)
17-36943008-C-T		LHX1-related disorder	Benign (Nov 28, 2023)
17-36943021-G-A		Inborn genetic diseases	Uncertain significance (Jan 18, 2023)
17-36943059-G-A			Likely benign (Oct 01, 2022)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential transcription factor. May play a role in early mesoderm formation and later in lateral mesoderm differentiation and neurogenesis. {ECO:0000269|PubMed:9212161}.
• Pathway: Neural Crest Differentiation;Endoderm Differentiation;Ectoderm Differentiation (Consensus)

Recessive Scores

• pRec: 0.335

Intolerance Scores

• loftool: 0.0767
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.51

Haploinsufficiency Scores

• pHI: 0.866
• hipred: Y
• hipred_score: 0.648

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.958

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Lhx1
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); renal/urinary system phenotype; embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); growth/size/body region phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: urogenital system development;ureteric bud development;branching involved in ureteric bud morphogenesis;gastrulation with mouth forming second;ectoderm formation;endoderm formation;kidney development;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;cell-cell signaling;pattern specification process;nervous system development;motor neuron axon guidance;anatomical structure morphogenesis;post-embryonic development;embryonic pattern specification;animal organ morphogenesis;anterior/posterior axis specification;anterior/posterior pattern specification;dorsal/ventral pattern formation;regulation of gene expression;retina layer formation;ventral spinal cord development;spinal cord association neuron differentiation;telencephalon development;cerebellum development;cerebellar Purkinje cell differentiation;forebrain regionalization;cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation;somite rostral/caudal axis specification;metanephric part of ureteric bud development;oviduct epithelium development;uterine epithelium development;nephric duct elongation;horizontal cell localization;positive regulation of embryonic development;cellular response to fibroblast growth factor stimulus;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;anatomical structure formation involved in morphogenesis;embryonic viscerocranium morphogenesis;pronephros development;embryonic retina morphogenesis in camera-type eye;uterus development;oviduct development;cervix development;vagina development;head development;epithelium development;paramesonephric duct development;comma-shaped body morphogenesis;S-shaped body morphogenesis;renal vesicle morphogenesis;mesonephric duct development;nephric duct morphogenesis;metanephric glomerulus development;metanephric comma-shaped body morphogenesis;metanephric renal vesicle morphogenesis;metanephric S-shaped body morphogenesis;primitive streak formation;positive regulation of branching involved in ureteric bud morphogenesis;dorsal spinal cord interneuron posterior axon guidance;lateral motor column neuron migration;positive regulation of gastrulation;positive regulation of anterior head development;positive regulation of nephron tubule epithelial cell differentiation
• Cellular component: nucleus;protein-containing complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;transcription corepressor activity;sequence-specific DNA binding;metal ion binding