CEBPB
CCAAT enhancer binding protein beta, the group of CCAAT/enhancer binding proteins |Basic leucine zipper proteins
Basic information
Region (hg38): 20:50190734-50192690
Previous symbols: [ "TCF5" ]
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 CEBPB 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 | 25 | 25 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 25 | 1 | 0 |
Variants in CEBPB
This is a list of pathogenic ClinVar variants found in the CEBPB region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 20-50191076-C-T | not specified | Uncertain significance (Dec 15, 2023) | ||
| 20-50191078-G-A | Likely benign (Jun 12, 2018) | |||
| 20-50191148-G-A | not specified | Uncertain significance (Oct 10, 2023) | ||
| 20-50191179-C-T | not specified | Uncertain significance (Oct 20, 2021) | ||
| 20-50191192-A-C | not specified | Uncertain significance (Jul 20, 2021) | ||
| 20-50191254-A-C | not specified | Uncertain significance (Nov 11, 2024) | ||
| 20-50191291-G-C | not specified | Uncertain significance (Mar 13, 2023) | ||
| 20-50191308-C-G | not specified | Uncertain significance (May 23, 2024) | ||
| 20-50191317-A-C | not specified | Uncertain significance (Jan 21, 2025) | ||
| 20-50191350-C-A | not specified | Uncertain significance (Aug 04, 2023) | ||
| 20-50191405-C-A | not specified | Uncertain significance (Jul 09, 2024) | ||
| 20-50191406-G-A | not specified | Uncertain significance (Nov 27, 2023) | ||
| 20-50191407-A-G | not specified | Uncertain significance (Feb 15, 2023) | ||
| 20-50191472-G-C | not specified | Uncertain significance (Jun 03, 2024) | ||
| 20-50191526-C-G | not specified | Uncertain significance (Sep 15, 2021) | ||
| 20-50191538-C-T | not specified | Uncertain significance (Jun 07, 2024) | ||
| 20-50191539-C-T | not specified | Uncertain significance (Dec 28, 2022) | ||
| 20-50191611-C-G | not specified | Uncertain significance (Oct 22, 2021) | ||
| 20-50191704-T-G | not specified | Uncertain significance (Jan 02, 2025) | ||
| 20-50191755-C-T | not specified | Uncertain significance (Jul 19, 2023) | ||
| 20-50191782-C-T | not specified | Uncertain significance (May 31, 2023) | ||
| 20-50191785-G-A | not specified | Uncertain significance (Mar 30, 2024) | ||
| 20-50191790-G-A | not specified | Uncertain significance (Nov 29, 2024) | ||
| 20-50191794-C-G | not specified | Uncertain significance (Nov 10, 2022) | ||
| 20-50191847-G-A | not specified | Uncertain significance (Oct 25, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CEBPB | protein_coding | protein_coding | ENST00000303004 | 1 | 1837 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.358 | 0.594 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.897 | 92 | 120 | 0.769 | 0.00000557 | 2122 |
| Missense in Polyphen | 17 | 39.395 | 0.43152 | 599 | ||
| Synonymous | -1.76 | 74 | 57.1 | 1.30 | 0.00000291 | 728 |
| Loss of Function | 1.56 | 1 | 4.61 | 0.217 | 1.96e-7 | 86 |
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) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Important transcription factor regulating the expression of genes involved in immune and inflammatory responses (PubMed:1741402, PubMed:9374525, PubMed:12048245, PubMed:18647749). Plays also a significant role in adipogenesis, as well as in the gluconeogenic pathway, liver regeneration, and hematopoiesis. The consensus recognition site is 5'- T[TG]NNGNAA[TG]-3'. Its functional capacity is governed by protein interactions and post-translational protein modifications. During early embryogenesis, plays essential and redundant functions with CEBPA. Has a promitotic effect on many cell types such as hepatocytes and adipocytes but has an antiproliferative effect on T-cells by repressing MYC expression, facilitating differentiation along the T-helper 2 lineage. Binds to regulatory regions of several acute-phase and cytokines genes and plays a role in the regulation of acute-phase reaction and inflammation. Plays also a role in intracellular bacteria killing (By similarity). During adipogenesis, is rapidly expressed and, after activation by phosphorylation, induces CEBPA and PPARG, which turn on the series of adipocyte genes that give rise to the adipocyte phenotype. The delayed transactivation of the CEBPA and PPARG genes by CEBPB appears necessary to allow mitotic clonal expansion and thereby progression of terminal differentiation (PubMed:20829347). Essential for female reproduction because of a critical role in ovarian follicle development (By similarity). Restricts osteoclastogenesis: together with NFE2L1; represses expression of DSPP during odontoblast differentiation (By similarity). {ECO:0000250|UniProtKB:P21272, ECO:0000250|UniProtKB:P28033, ECO:0000269|PubMed:12048245, ECO:0000269|PubMed:18647749, ECO:0000269|PubMed:20829347, ECO:0000269|PubMed:9374525, ECO:0000303|PubMed:25451943}.; FUNCTION: Isoform 3: Acts as a dominant negative through heterodimerization with isoform 2 (PubMed:11741938). Promotes osteoblast differentiation and osteoclastogenesis (By similarity). {ECO:0000250|UniProtKB:P21272, ECO:0000250|UniProtKB:P28033, ECO:0000269|PubMed:11741938}.;
- Pathway
- TNF signaling pathway - Homo sapiens (human);Tuberculosis - Homo sapiens (human);IL-17 signaling pathway - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Folate-Alcohol and Cancer Pathway Hypotheses;miR-targeted genes in adipocytes - TarBase;miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Transcriptional regulation of white adipocyte differentiation;IL17 signaling pathway;White fat cell differentiation;Adipogenesis;Oncostatin M Signaling Pathway;Differentiation of white and brown adipocyte;Transcriptional activation by NRF2;Senescence-Associated Secretory Phenotype (SASP);Ovarian Infertility Genes;Transcription factor regulation in adipogenesis;Lung fibrosis;IL-4 Signaling Pathway;Exercise-induced Circadian Regulation;White fat cell differentiation;Transcriptional cascade regulating adipogenesis;Senescence and Autophagy in Cancer;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;il 6 signaling pathway;Senescence-Associated Secretory Phenotype (SASP);Cellular Senescence;Cellular responses to stress;TCR;Oncostatin_M;Cellular responses to external stimuli;EGFR1;FOXA1 transcription factor network;C-MYB transcription factor network;IFN-gamma pathway;IL4;IL6;Signaling mediated by p38-alpha and p38-beta;Validated nuclear estrogen receptor alpha network;IL4-mediated signaling events;Regulation of retinoblastoma protein;FOXA2 and FOXA3 transcription factor networks;Regulation of nuclear SMAD2/3 signaling;IL6-mediated signaling events;IL3-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.107
Haploinsufficiency Scores
- pHI
- 0.981
- hipred
- Y
- hipred_score
- 0.553
- ghis
- 0.584
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cebpb
- Phenotype
- hematopoietic system 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; neoplasm; liver/biliary system phenotype; immune system phenotype; skeleton phenotype; renal/urinary system phenotype; craniofacial phenotype; vision/eye phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;ovarian follicle development;embryonic placenta development;regulation of transcription, DNA-templated;transcription by RNA polymerase II;acute-phase response;inflammatory response;immune response;memory;neuron differentiation;positive regulation of interleukin-4 production;mammary gland epithelial cell proliferation;response to endoplasmic reticulum stress;negative regulation of T cell proliferation;defense response to bacterium;negative regulation of neuron apoptotic process;regulation of interleukin-6 biosynthetic process;positive regulation of fat cell differentiation;positive regulation of osteoblast differentiation;regulation of osteoclast differentiation;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of inflammatory response;brown fat cell differentiation;mammary gland epithelial cell differentiation;regulation of transcription involved in cell fate commitment;intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress;positive regulation of biomineral tissue development;cellular response to lipopolysaccharide;cellular response to amino acid stimulus;cellular response to interleukin-1;cellular response to organic cyclic compound;hepatocyte proliferation;liver regeneration;positive regulation of cold-induced thermogenesis;regulation of odontoblast differentiation;positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress;positive regulation of sodium-dependent phosphate transport;regulation of dendritic cell differentiation
- Cellular component
- condensed chromosome, centromeric region;nuclear chromatin;nucleus;nucleoplasm;cytoplasm;nuclear matrix;CHOP-C/EBP complex
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;RNA polymerase II core promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;chromatin binding;DNA-binding transcription factor activity;protein binding;kinase binding;histone acetyltransferase binding;glucocorticoid receptor binding;protein homodimerization activity;histone deacetylase binding;ubiquitin-like protein ligase binding;protein heterodimerization activity