CEBPE

CCAAT enhancer binding protein epsilon, the group of CCAAT/enhancer binding proteins |Basic leucine zipper proteins

Basic information

Region (hg38): 14:23117036-23120256

Links

ENSG00000092067 ∙ NCBI:1053 ∙ OMIM:600749 ∙ HGNC:1836 ∙ Uniprot:Q15744 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• specific granule deficiency (Supportive), mode of inheritance: AR
• specific granule deficiency 1 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Specific granule deficiency 1; Immunodeficiency 108 with autoinflammation	AR	Allergy/Immunology/Infectious	Individuals with Specific granule deficiency have severe immunocompromise, and antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficial; Immunodeficiency108 with autoinflammation involves immunodeficiency, and antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficia	Allergy/Immunology/Infectious	10359588; 11313242; 31201888

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CEBPE gene.

• Specific granule deficiency (4 variants)
• Specific granule deficiency 1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEBPE 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			2	64	4	70
missense		1	97	2		100
nonsense	2	1				3
start loss						0
frameshift	2		1			3
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			1	1		2
non coding				5	2	7
Total	4	2	101	71	6

Variants in CEBPE

This is a list of pathogenic ClinVar variants found in the CEBPE region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
14-23117491-C-T		Specific granule deficiency • Specific granule deficiency 1 • CEBPE-related disorder	Conflicting classifications of pathogenicity (Jan 29, 2024)
14-23117500-C-T		Inborn genetic diseases	Uncertain significance (Dec 13, 2021)
14-23117504-C-T			Uncertain significance (Oct 01, 2021)
14-23117505-G-A		Specific granule deficiency • CEBPE-related disorder	Likely benign (Nov 25, 2023)
14-23117513-T-C		Specific granule deficiency	Uncertain significance (Aug 03, 2020)
14-23117520-G-A		Specific granule deficiency	Likely benign (Oct 17, 2022)
14-23117523-C-T		Specific granule deficiency	Likely benign (Nov 07, 2022)
14-23117529-A-G		Specific granule deficiency	Likely benign (Jun 20, 2022)
14-23117535-C-T		Specific granule deficiency	Likely benign (Apr 10, 2023)
14-23117538-G-C		Specific granule deficiency	Likely benign (Oct 02, 2021)
14-23117539-C-T		Specific granule deficiency	Uncertain significance (Aug 19, 2022)
14-23117540-G-A		Inborn genetic diseases	Uncertain significance (Aug 22, 2023)
14-23117543-A-C		Inborn genetic diseases	Uncertain significance (Jan 08, 2024)
14-23117544-G-C		Specific granule deficiency	Likely benign (May 04, 2019)
14-23117554-A-C		Specific granule deficiency	Uncertain significance (Apr 06, 2022)
14-23117555-G-A		Specific granule deficiency	Uncertain significance (Aug 01, 2022)
14-23117561-C-T		Specific granule deficiency	Uncertain significance (Dec 14, 2023)
14-23117585-CGCGGCT-C		Specific granule deficiency 1	Pathogenic (Sep 15, 2022)
14-23117586-G-A		Specific granule deficiency • CEBPE-related disorder	Benign (Jan 31, 2024)
14-23117591-T-G		Inborn genetic diseases	Uncertain significance (Nov 30, 2022)
14-23117593-C-T		Specific granule deficiency	Uncertain significance (Jun 13, 2022)
14-23117600-G-A		Specific granule deficiency	Uncertain significance (Jun 09, 2022)
14-23117604-G-A		Specific granule deficiency	Likely benign (Aug 10, 2022)
14-23117610-T-C		Specific granule deficiency	Likely benign (Feb 19, 2022)
14-23117612-C-T		Specific granule deficiency	Uncertain significance (Jul 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEBPE	protein_coding	protein_coding	ENST00000206513	2	2313

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00708	0.927	125726	0	16	125742	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.233	180	189	0.952	0.0000131	1788
Missense in Polyphen		84	87.333	0.96184		858
Synonymous	-0.705	90	81.9	1.10	0.00000577	609
Loss of Function	1.59	5	10.6	0.473	8.07e-7	97

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.0000728	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000988	0.0000980
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional activator (PubMed:26019275). C/EBP are DNA-binding proteins that recognize two different motifs: the CCAAT homology common to many promoters and the enhanced core homology common to many enhancers. Required for the promyelocyte- myelocyte transition in myeloid differentiation (PubMed:10359588). {ECO:0000269|PubMed:10359588, ECO:0000269|PubMed:26019275}.
• Disease: DISEASE: Specific granule deficiency 1 (SGD1) [MIM:245480]: An autosomal recessive disorder characterized by recurrent pyogenic infections, defective neutrophil chemotaxis and bactericidal activity, and lack of neutrophil secondary granule proteins. Neutrophils of affected individuals lack lactoferrin and show abnormal nuclear segmentation, bilobed nuclei, low alkaline phosphatase, and increased number of neutrophil mitochondria and ribosomes. {ECO:0000269|PubMed:10359588, ECO:0000269|PubMed:11313242, ECO:0000269|PubMed:26019275}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Acute myeloid leukemia - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.213

Intolerance Scores

• loftool: 0.507
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.69

Haploinsufficiency Scores

• pHI: 0.483
• hipred: N
• hipred_score: 0.339
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.944

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cebpe
• Phenotype: cellular 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); respiratory system phenotype; immune system phenotype; skeleton phenotype; digestive/alimentary phenotype; vision/eye 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); hematopoietic system phenotype

Gene ontology

• Biological process: phagocytosis;defense response;macrophage differentiation;granulocyte differentiation;cytokine biosynthetic process;defense response to bacterium;positive regulation of transcription by RNA polymerase II;cellular response to lipopolysaccharide
• Cellular component: nucleus;nucleoplasm
• 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;protein homodimerization activity;protein heterodimerization activity