ZBED1
protein-codingzinc finger BED-type containing 1, the group of Zinc fingers BED-type|Pseudoautosomal region 1
Gene summary
This gene is located in the pseudoautosomal region 1 (PAR1) of X and Y chromosomes. It was earlier identified as a gene with similarity to Ac transposable elements, however, was found not to have transposase activity. Later studies show that this gene product is localized in the nucleus and functions as a transcription factor. It binds to DNA elements found in the promoter regions of several genes related to cell proliferation, such as histone H1, hence may have a role in regulating genes related to cell proliferation. Alternatively spliced transcript variants with different 5' untranslated region have been found for this gene. [provided by RefSeq, Jan 2010]
- ALTE
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~14.6 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 ZBED1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001171136.2. 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 | 0 | |||||
| missense | 1 | 1 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 0 | 0 | 1 | 1 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001164607.1 | 2 | MANE Select | |
| Ensembl | ENSP00000498725.1 | 1 | MANE Select | |
| RefSeq | NP_001164606.1 | 2 | Standard | |
| RefSeq | NP_004720.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- SUMOylation of chromatin organization proteins
- Post-translational protein modification
- SUMO E3 ligases SUMOylate target proteins
- Metabolism of proteins
- SUMOylation
Biological Process
- protein sumoylation
- positive regulation of transcription by RNA polymerase II
Molecular Function
- RNA polymerase II proximal promoter sequence-specific DNA binding
- DNA-binding transcription factor activity, RNA polymerase II-specific
- DNA-binding transcription activator activity, RNA polymerase II-specific
- protein binding
- SUMO transferase activity
Cellular Component
- nuclear chromosome
- nucleoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000381223
- Coding exons
- 1
- Length
- 14554
- Individuals with no LoFs
- 125557
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 34
- Defined
- 125591
- p
- 0.000135
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.847 | 404 | 455 | 0.888 | 0.0000344 | 4564 |
| Missense (PolyPhen) | 99 | 139.71 | 0.70861 | 1504 | ||
| Synonymous | -0.999 | 245 | 226 | 1.08 | 0.0000200 | 1410 |
| Loss of Function | 2.29 | 9 | 20.1 | 0.448 | 9.76e-7 | 221 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.00017 | 0.00017 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0.00019 | 0.00018 | rare |
| European (Non-Finnish) | 0.00013 | 0.00012 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Binds to 5'-TGTCG[CT]GA[CT]A-3' DNA elements found in the promoter regions of a number of genes related to cell proliferation. Binds to the histone H1 promoter and stimulates transcription. Was first identified as gene weakly similar to Ac transposable elements, but does not code for any transposase activity. {ECO:0000269|PubMed:12663651}.;
Recessive Scores
- pRec
- 0.163
Intolerance Scores
- LoFtool
- 0.142
- RVIS EVS
- -2.19
- RVIS percentile EVS
- 1.39
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.972
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |