LHX1
LIM homeobox 1, the group of LIM class homeoboxes
Basic information
Region (hg38): 17:36936785-36944612
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn_genetic_diseases (40 variants)
- LHX1-related_disorder (10 variants)
- not_provided (2 variants)
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. These statistics are base on transcript: NM_000005568.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 9 | |||||
| missense | 40 | 42 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 40 | 7 | 4 |
Loading clinvar variants...
GnomAD
Source:
dbNSFP
Source:
- 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
- ghis
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