LDB1
LIM domain binding 1, the group of Wnt enhanceosome complex
Basic information
Region (hg38): 10:102106489-102120368
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LDB1 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 | 0 | |||||
| missense | 15 | 16 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 15 | 1 | 0 |
Variants in LDB1
This is a list of pathogenic ClinVar variants found in the LDB1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 10-102108130-C-T | not specified | Uncertain significance (Aug 13, 2021) | ||
| 10-102108204-C-G | not specified | Uncertain significance (Dec 05, 2022) | ||
| 10-102108272-C-T | not specified | Uncertain significance (Feb 05, 2024) | ||
| 10-102108314-C-T | not specified | Uncertain significance (Dec 17, 2023) | ||
| 10-102109115-T-C | not specified | Uncertain significance (Dec 02, 2022) | ||
| 10-102109124-C-A | not specified | Uncertain significance (Feb 16, 2023) | ||
| 10-102109166-G-A | not specified | Uncertain significance (May 05, 2023) | ||
| 10-102109467-C-T | not specified | Uncertain significance (May 18, 2022) | ||
| 10-102109622-T-C | not specified | Uncertain significance (Feb 13, 2024) | ||
| 10-102109666-C-A | not specified | Uncertain significance (Feb 06, 2023) | ||
| 10-102110571-C-A | not specified | Uncertain significance (Oct 26, 2022) | ||
| 10-102110578-C-G | not specified | Uncertain significance (Jul 19, 2023) | ||
| 10-102110655-C-A | Likely benign (Mar 01, 2023) | |||
| 10-102111121-T-G | not specified | Uncertain significance (Nov 17, 2022) | ||
| 10-102111438-C-T | not specified | Uncertain significance (Apr 28, 2022) | ||
| 10-102111486-C-T | not specified | Uncertain significance (Sep 25, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LDB1 | protein_coding | protein_coding | ENST00000425280 | 11 | 12894 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.985 | 0.0147 | 125743 | 0 | 1 | 125744 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.81 | 132 | 259 | 0.509 | 0.0000161 | 2741 |
| Missense in Polyphen | 40 | 112.95 | 0.35415 | 1113 | ||
| Synonymous | 0.0546 | 98 | 98.7 | 0.993 | 0.00000663 | 745 |
| Loss of Function | 3.91 | 2 | 21.6 | 0.0925 | 0.00000109 | 247 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000176 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Binds to the LIM domain of a wide variety of LIM domain- containing transcription factors. May regulate the transcriptional activity of LIM-containing proteins by determining specific partner interactions. Plays a role in the development of interneurons and motor neurons in cooperation with LHX3 and ISL1. Acts synergistically with LHX1/LIM1 in axis formation and activation of gene expression. Acts with LMO2 in the regulation of red blood cell development, maintaining erythroid precursors in an immature state (By similarity). {ECO:0000250|UniProtKB:P70662}.;
- Pathway
- Transcriptional misregulation in cancer - Homo sapiens (human);Developmental Biology;Gene expression (Transcription);multi-step regulation of transcription by pitx2;Generic Transcription Pathway;RNA Polymerase II Transcription;Regulation of expression of SLITs and ROBOs;Signaling by ROBO receptors;Axon guidance;RUNX1 regulates transcription of genes involved in differentiation of HSCs;Transcriptional regulation by RUNX1
(Consensus)
Recessive Scores
- pRec
- 0.186
Intolerance Scores
- loftool
- 0.0572
- rvis_EVS
- -0.43
- rvis_percentile_EVS
- 25.15
Haploinsufficiency Scores
- pHI
- 0.862
- hipred
- Y
- hipred_score
- 0.775
- ghis
- 0.612
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.943
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ldb1
- Phenotype
- growth/size/body region phenotype; craniofacial phenotype; homeostasis/metabolism phenotype; renal/urinary system phenotype; embryo 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; reproductive system 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); hematopoietic system 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); digestive/alimentary phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery;gastrulation with mouth forming second;hair follicle development;transcription, DNA-templated;regulation of transcription, DNA-templated;transcription by RNA polymerase II;multicellular organism development;anterior/posterior axis specification;epithelial structure maintenance;Wnt signaling pathway;cerebellar Purkinje cell differentiation;cellular component assembly;neuron differentiation;regulation of cell migration;regulation of DNA-templated transcription, elongation;somatic stem cell population maintenance;regulation of kinase activity;histone H3-K4 acetylation;negative regulation of erythrocyte differentiation;positive regulation of cell adhesion;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of hemoglobin biosynthetic process;regulation of focal adhesion assembly;regulation of hematopoietic stem cell differentiation
- Cellular component
- nuclear chromatin;nucleus;nucleoplasm;transcription factor complex;cell leading edge;protein-containing complex;beta-catenin-TCF complex
- Molecular function
- RNA polymerase II activating transcription factor binding;enhancer sequence-specific DNA binding;chromatin binding;transcription corepressor activity;protein binding;enzyme binding;LIM domain binding;protein homodimerization activity;protein self-association