E4F1

E4F transcription factor 1, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 16:2223580-2235742

Links

ENSG00000167967 ∙ NCBI:1877 ∙ OMIM:603022 ∙ HGNC:3121 ∙ Uniprot:Q66K89 ∙ 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 E4F1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the E4F1 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		2
missense			49	3		52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	49	5	0

Variants in E4F1

This is a list of pathogenic ClinVar variants found in the E4F1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-2223641-A-T		not specified	Uncertain significance (Aug 10, 2021)
16-2223656-G-A		not specified	Uncertain significance (Nov 03, 2022)
16-2223695-G-A		not specified	Uncertain significance (Aug 12, 2024)
16-2223699-C-T		not specified	Uncertain significance (Jan 29, 2024)
16-2223724-G-C		not specified	Uncertain significance (Oct 27, 2023)
16-2223769-A-C		not specified	Uncertain significance (Dec 18, 2023)
16-2228373-T-A		not specified	Uncertain significance (Dec 02, 2022)
16-2228399-G-A		not specified	Uncertain significance (Jun 11, 2024)
16-2228465-G-A		not specified	Uncertain significance (Feb 17, 2022)
16-2228471-C-T		not specified	Uncertain significance (Feb 05, 2024)
16-2228493-C-G			Likely benign (Jun 01, 2022)
16-2228507-C-G		not specified	Uncertain significance (Nov 07, 2022)
16-2228516-G-A		not specified	Uncertain significance (Jul 11, 2022)
16-2228519-A-G		not specified	Uncertain significance (Jun 29, 2022)
16-2229586-C-T		not specified	Uncertain significance (Jun 26, 2024)
16-2229631-C-T		not specified	Uncertain significance (Jan 10, 2023)
16-2229636-T-C		not specified	Uncertain significance (Jun 13, 2024)
16-2229655-G-A		not specified	Uncertain significance (May 14, 2024)
16-2229660-G-A		not specified	Likely benign (Oct 26, 2022)
16-2229663-T-C		not specified	Likely benign (May 22, 2023)
16-2232186-A-G		not specified	Uncertain significance (Sep 30, 2024)
16-2232192-T-A		not specified	Uncertain significance (Apr 04, 2024)
16-2232210-C-T		not specified	Uncertain significance (Nov 13, 2024)
16-2232243-C-T		not specified	Uncertain significance (Jun 29, 2022)
16-2232263-G-C		not specified	Uncertain significance (Aug 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
E4F1	protein_coding	protein_coding	ENST00000301727	14	12177

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0801	0.920	125609	0	13	125622	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.35	424	510	0.832	0.0000346	4988
Missense in Polyphen		161	222.46	0.72373		2140
Synonymous	-2.39	279	233	1.20	0.0000177	1637
Loss of Function	3.75	8	30.3	0.264	0.00000146	364

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000875	0.0000875
Ashkenazi Jewish	0.00	0.00
East Asian	0.000123	0.0000544
Finnish	0.0000468	0.0000462
European (Non-Finnish)	0.0000649	0.0000616
Middle Eastern	0.000123	0.0000544
South Asian	0.0000693	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as a transcriptional repressor. May also function as a ubiquitin ligase mediating ubiquitination of chromatin-associated TP53. Functions in cell survival and proliferation through control of the cell cycle. Functions in the p53 and pRB tumor suppressor pathways and regulates the cyclin CCNA2 transcription.
• Pathway: p53 pathway (Consensus)

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.187
• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.24

Haploinsufficiency Scores

• pHI: 0.785
• hipred: Y
• hipred_score: 0.669
• ghis: 0.554

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.654

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: E4f1
• 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); embryo 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); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: e4f1
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: kinked

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;DNA replication;cell population proliferation;regulation of mitotic cell cycle, embryonic;regulation of cell cycle process;viral process;protein ubiquitination;regulation of growth;cell division;mitotic cell cycle arrest;positive regulation of nucleic acid-templated transcription
• Cellular component: nucleoplasm;cytoplasm;spindle
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;transcription coactivator activity;transcription corepressor activity;protein binding;transferase activity;cAMP response element binding;metal ion binding