CEBPD

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

Basic information

Region (hg38): 8:47736913-47738164

Links

ENSG00000221869 ∙ NCBI:1052 ∙ OMIM:116898 ∙ HGNC:1835 ∙ Uniprot:P49716 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CEBPD 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			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	0

Variants in CEBPD

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

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

Position	Type	Phenotype	Significance	ClinVar
8-47737367-T-C		not specified	Uncertain significance (Dec 21, 2022)
8-47737379-G-A		not specified	Uncertain significance (Feb 22, 2023)
8-47737384-C-T		not specified	Uncertain significance (Aug 04, 2023)
8-47737404-C-G		not specified	Uncertain significance (Apr 22, 2024)
8-47737414-C-T		not specified	Uncertain significance (Jun 17, 2022)
8-47737466-T-C		not specified	Uncertain significance (Oct 02, 2023)
8-47737471-T-C		not specified	Uncertain significance (Jul 20, 2021)
8-47737517-T-G		not specified	Uncertain significance (Dec 22, 2023)
8-47737524-C-G		not specified	Uncertain significance (Jul 25, 2023)
8-47737553-C-G		not specified	Uncertain significance (Dec 08, 2023)
8-47737592-C-T		not specified	Uncertain significance (Jan 17, 2024)
8-47737601-G-T		not specified	Uncertain significance (Sep 16, 2021)
8-47737603-G-A		not specified	Uncertain significance (Jan 26, 2022)
8-47737609-G-T		not specified	Uncertain significance (Aug 08, 2022)
8-47737616-T-C		not specified	Likely benign (Aug 12, 2021)
8-47737711-G-A		not specified	Uncertain significance (May 28, 2024)
8-47737726-C-T		not specified	Uncertain significance (Dec 03, 2021)
8-47737727-C-T		not specified	Uncertain significance (Apr 28, 2023)
8-47737732-G-A		not specified	Uncertain significance (Jun 17, 2024)
8-47737775-G-C		not specified	Uncertain significance (Aug 08, 2023)
8-47737786-C-T		not specified	Uncertain significance (Sep 20, 2023)
8-47737828-A-C		not specified	Uncertain significance (Nov 16, 2021)
8-47737848-C-G		not specified	Uncertain significance (Dec 03, 2021)
8-47737855-T-C		not specified	Uncertain significance (Aug 28, 2023)
8-47737897-T-C		not specified	Uncertain significance (Aug 04, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CEBPD	protein_coding	protein_coding	ENST00000408965	1	2178

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.612	0.356	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.317	88	96.8	0.909	0.00000448	1676
Missense in Polyphen		35	41.57	0.84196		663
Synonymous	0.00846	44	44.1	0.998	0.00000209	573
Loss of Function	1.60	0	3.00	0.00	1.28e-7	58

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: dbNSFP

• Function: FUNCTION: Transcription activator that recognizes two different DNA motifs: the CCAAT homology common to many promoters and the enhanced core homology common to many enhancers (PubMed:16397300). Important transcription factor regulating the expression of genes involved in immune and inflammatory responses (PubMed:1741402, PubMed:16397300). Transcriptional activator that enhances IL6 transcription alone and as heterodimer with CEBPB (PubMed:1741402). {ECO:0000269|PubMed:1741402}.
• Pathway: Transcriptional regulation of white adipocyte differentiation;IL17 signaling pathway;White fat cell differentiation;Adipogenesis;MECP2 and Associated Rett Syndrome;Transcription factor regulation in adipogenesis;Interleukin-4 and 13 signaling;White fat cell differentiation;Transcriptional cascade regulating adipogenesis;C-MYB transcription factor network;Validated targets of C-MYC transcriptional repression;Validated transcriptional targets of deltaNp63 isoforms;Regulation of retinoblastoma protein;FOXA2 and FOXA3 transcription factor networks;IL6-mediated signaling events (Consensus)

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.621
• ghis: 0.461

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.825

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cebpd
• Phenotype: renal/urinary system phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system 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); 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); homeostasis/metabolism phenotype; cellular phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype

Gene ontology

• Biological process: transcription by RNA polymerase II;cytokine-mediated signaling pathway;positive regulation of transcription by RNA polymerase II
• Cellular component: 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