LHX1
protein-codingLIM homeobox 1, the group of LIM class homeoboxes
Gene summary
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. [provided by RefSeq, Dec 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~7.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to LHX1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005568.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 7 | 3 | 10 | |||
| missense | 43 | 1 | 1 | 45 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 43 | 8 | 4 | 55 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005559.2 | 5 | MANE Select | |
| Ensembl | ENSP00000477829.1 | 5 | MANE Select | |
| Ensembl | ENSP00000481496.1 | 2 | Standard | |
| Ensembl | ENSP00000569149.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Neural Crest Differentiation
- Endoderm Differentiation
- Ectoderm Differentiation
Biological Process
- urogenital system development
- ureteric bud development
- branching involved in ureteric bud morphogenesis
- gastrulation with mouth forming second
- ectoderm formation
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
Cellular Component
- nucleus
- protein-containing complex
dbNSFP Gene Annotations
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}.;
Recessive Scores
- pRec
- 0.335
Intolerance Scores
- LoFtool
- 0.0767
- RVIS EVS
- 0.15
- RVIS percentile EVS
- 64.51
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.958
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |