LDB2
Basic information
Region (hg38): 4:16501541-16898678
Links
Phenotypes
GenCC
Source:
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 LDB2 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 | 1 | |||||
| missense | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 0 | 1 |
Variants in LDB2
This is a list of pathogenic ClinVar variants found in the LDB2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-16502759-C-T | not specified | Uncertain significance (Nov 07, 2023) | ||
| 4-16502764-A-C | not specified | Uncertain significance (May 30, 2023) | ||
| 4-16502776-G-T | not specified | Uncertain significance (Dec 05, 2022) | ||
| 4-16508669-G-C | not specified | Uncertain significance (May 14, 2024) | ||
| 4-16511990-C-A | not specified | Uncertain significance (Jan 18, 2022) | ||
| 4-16512098-C-T | not specified | Uncertain significance (Dec 03, 2021) | ||
| 4-16588771-G-A | not specified | Uncertain significance (Oct 13, 2023) | ||
| 4-16595714-T-C | not specified | Uncertain significance (Dec 15, 2022) | ||
| 4-16595821-A-G | not specified | Uncertain significance (Sep 30, 2021) | ||
| 4-16595825-C-A | EBV-positive nodal T- and NK-cell lymphoma | Likely benign (-) | ||
| 4-16759189-T-C | Benign (May 03, 2018) | |||
| 4-16898413-T-C | not specified | Uncertain significance (Dec 05, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LDB2 | protein_coding | protein_coding | ENST00000304523 | 8 | 397269 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.955 | 0.0454 | 125731 | 0 | 3 | 125734 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.37 | 118 | 216 | 0.546 | 0.0000116 | 2479 |
| Missense in Polyphen | 34 | 77.394 | 0.43931 | 872 | ||
| Synonymous | 0.317 | 82 | 85.7 | 0.956 | 0.00000573 | 686 |
| Loss of Function | 3.56 | 2 | 18.5 | 0.108 | 8.75e-7 | 217 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000943 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000367 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Binds to the LIM domain of a wide variety of LIM domain- containing transcription factors.;
- Pathway
- Ectoderm Differentiation
(Consensus)
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- 0.0432
- rvis_EVS
- -0.47
- rvis_percentile_EVS
- 23.04
Haploinsufficiency Scores
- pHI
- 0.928
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.667
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.983
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ldb2
- Phenotype
- normal phenotype;
Zebrafish Information Network
- Gene name
- ldb2a
- Affected structure
- nodal signaling pathway
- Phenotype tag
- abnormal
- Phenotype quality
- increased process quality
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;hair follicle development;multicellular organism development;epithelial structure maintenance;regulation of cell migration;somatic stem cell population maintenance;regulation of kinase activity;positive regulation of cellular component biogenesis;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
- Cellular component
- nucleus;transcription factor complex;nucleolus;plasma membrane;cell leading edge
- Molecular function
- RNA polymerase II activating transcription factor binding;transcription coregulator activity;protein binding;enzyme binding;LIM domain binding