CITED4

Cbp/p300 interacting transactivator with Glu/Asp rich carboxy-terminal domain 4

Basic information

Region (hg38): 1:40861054-40862363

Links

ENSG00000179862 ∙ NCBI:163732 ∙ OMIM:606815 ∙ HGNC:18696 ∙ Uniprot:Q96RK1 ∙ 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 CITED4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CITED4 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			26
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	0	0

Variants in CITED4

This is a list of pathogenic ClinVar variants found in the CITED4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-40861583-A-C		not specified	Uncertain significance (Mar 21, 2023)
1-40861653-C-T		not specified	Uncertain significance (Mar 29, 2023)
1-40861665-G-A		not specified	Uncertain significance (Mar 01, 2023)
1-40861665-G-C		not specified	Uncertain significance (Dec 10, 2024)
1-40861722-G-C		not specified	Uncertain significance (Aug 10, 2021)
1-40861782-C-T		not specified	Uncertain significance (Jul 12, 2022)
1-40861787-T-G		not specified	Uncertain significance (Sep 17, 2021)
1-40861791-G-A		not specified	Uncertain significance (Dec 16, 2023)
1-40861844-G-C		not specified	Uncertain significance (Sep 14, 2022)
1-40861850-G-T		not specified	Uncertain significance (Feb 28, 2023)
1-40861854-C-G		not specified	Uncertain significance (Jan 29, 2024)
1-40861865-T-G		not specified	Uncertain significance (May 11, 2022)
1-40861872-T-C		not specified	Uncertain significance (Dec 11, 2023)
1-40861890-G-C		not specified	Uncertain significance (Aug 08, 2022)
1-40861952-G-T		not specified	Uncertain significance (Jul 18, 2024)
1-40861959-G-C		not specified	Uncertain significance (Dec 01, 2024)
1-40861967-G-A		not specified	Uncertain significance (Mar 17, 2023)
1-40861979-G-A		not specified	Uncertain significance (Dec 08, 2023)
1-40862030-G-A		not specified	Uncertain significance (May 24, 2023)
1-40862054-C-A		not specified	Uncertain significance (Aug 11, 2024)
1-40862055-C-A		not specified	Uncertain significance (Aug 11, 2024)
1-40862063-G-C		not specified	Uncertain significance (Apr 19, 2023)
1-40862075-G-C		not specified	Uncertain significance (Sep 12, 2023)
1-40862078-G-A		not specified	Uncertain significance (Mar 04, 2024)
1-40862087-A-C		not specified	Uncertain significance (Jul 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CITED4	protein_coding	protein_coding	ENST00000372638	1	1290

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.346	0.495	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.975	11	24.6	0.447	0.00000113	1068
Missense in Polyphen		2	10.582	0.18899		357
Synonymous	0.559	11	13.6	0.807	6.94e-7	428
Loss of Function	0.714	0	0.594	0.00	2.60e-8	22

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: Acts as transcriptional coactivator for TFAP2/AP-2. Enhances estrogen-dependent transactivation mediated by estrogen receptors. May function as an inhibitor of transactivation by HIF1A by disrupting HIF1A interaction with CREBBP. May be involved in regulation of gene expression during development and differentiation of blood cells, endothelial cells and mammary epithelial cells. {ECO:0000269|PubMed:11744733, ECO:0000269|PubMed:15342390}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Activation of the TFAP2 (AP-2) family of transcription factors;Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors (Consensus)

Haploinsufficiency Scores

• pHI: 0.239
• hipred: N
• hipred_score: 0.238
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.886

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cited4

Zebrafish Information Network

• Gene name: cited4b
• Affected structure: muscle cell
• Phenotype tag: abnormal
• Phenotype quality: increased occurrence

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;response to estrogen;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;nucleoplasm;cytoplasm
• Molecular function: transcription coactivator activity