E2F7

E2F transcription factor 7, the group of E2F transcription factors

Basic information

Region (hg38): 12:77021248-77065569

Links

ENSG00000165891 ∙ NCBI:144455 ∙ OMIM:612046 ∙ HGNC:23820 ∙ Uniprot:Q96AV8 ∙ 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 E2F7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the E2F7 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					5	5
missense			45	3	1	49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	3	6

Variants in E2F7

This is a list of pathogenic ClinVar variants found in the E2F7 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-77024062-T-C		not specified	Uncertain significance (Jun 17, 2022)
12-77024075-C-T			Benign (Apr 12, 2018)
12-77024081-C-G		not specified	Uncertain significance (May 17, 2023)
12-77024180-T-G			Benign (Jun 27, 2018)
12-77024184-G-A		not specified	Uncertain significance (Sep 09, 2021)
12-77025593-C-T		not specified	Likely benign (Dec 31, 2023)
12-77025594-G-A			Benign (Jun 27, 2018)
12-77025614-G-T		not specified	Uncertain significance (Jan 24, 2023)
12-77025646-G-C		not specified	Uncertain significance (May 27, 2022)
12-77025751-A-G		not specified	Likely benign (Apr 26, 2023)
12-77025785-G-T		not specified	Uncertain significance (Apr 12, 2024)
12-77025823-G-A		not specified	Uncertain significance (Nov 07, 2022)
12-77025886-A-G		not specified	Uncertain significance (Aug 03, 2022)
12-77025943-G-A		not specified	Uncertain significance (May 24, 2023)
12-77025955-G-A		not specified	Uncertain significance (Feb 15, 2023)
12-77025976-T-C		not specified	Uncertain significance (Jan 24, 2023)
12-77027888-G-A		not specified	Uncertain significance (Oct 20, 2023)
12-77027888-G-C		not specified	Uncertain significance (Dec 14, 2022)
12-77027978-G-A		not specified	Uncertain significance (Oct 21, 2021)
12-77027999-A-T		not specified	Uncertain significance (Oct 25, 2022)
12-77028078-G-A		not specified	Uncertain significance (Jan 26, 2023)
12-77028089-C-G			Benign (Apr 12, 2018)
12-77029905-C-T		not specified	Uncertain significance (Apr 18, 2023)
12-77029908-G-C		not specified	Uncertain significance (Jan 26, 2022)
12-77029928-A-G		not specified	Uncertain significance (Apr 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
E2F7	protein_coding	protein_coding	ENST00000322886	12	44334

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00683	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.63	393	495	0.794	0.0000266	5874
Missense in Polyphen		93	155.86	0.5967		1834
Synonymous	-0.604	205	194	1.06	0.0000111	1883
Loss of Function	4.87	5	36.9	0.135	0.00000180	472

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000112	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.000112	0.000109
South Asian	0.000131	0.000131
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Atypical E2F transcription factor that participates in various processes such as angiogenesis, polyploidization of specialized cells and DNA damage response. Mainly acts as a transcription repressor that binds DNA independently of DP proteins and specifically recognizes the E2 recognition site 5'- TTTC[CG]CGC-3'. Directly represses transcription of classical E2F transcription factors such as E2F1. Acts as a regulator of S-phase by recognizing and binding the E2-related site 5'-TTCCCGCC-3' and mediating repression of G1/S-regulated genes. Plays a key role in polyploidization of cells in placenta and liver by regulating the endocycle, probably by repressing genes promoting cytokinesis and antagonizing action of classical E2F proteins (E2F1, E2F2 and/or E2F3). Required for placental development by promoting polyploidization of trophoblast giant cells. Also involved in DNA damage response: up-regulated by p53/TP53 following genotoxic stress and acts as a downstream effector of p53/TP53-dependent repression by mediating repression of indirect p53/TP53 target genes involved in DNA replication. Acts as a promoter of sprouting angiogenesis, possibly by acting as a transcription activator: associates with HIF1A, recognizes and binds the VEGFA promoter, which is different from canonical E2 recognition site, and activates expression of the VEGFA gene. Acts as a negative regulator of keratinocyte differentiation. {ECO:0000269|PubMed:14633988, ECO:0000269|PubMed:15133492, ECO:0000269|PubMed:18202719, ECO:0000269|PubMed:19223542, ECO:0000269|PubMed:21248772, ECO:0000269|PubMed:22802528, ECO:0000269|PubMed:22802529, ECO:0000269|PubMed:22903062}.
• Pathway: Gastric Cancer Network 1;TP53 Regulates Transcription of Cell Cycle Genes;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest;TP53 Regulates Transcription of Cell Cycle Genes;Transcriptional Regulation by TP53;E2F transcription factor network (Consensus)

Recessive Scores

• pRec: 0.0974

Intolerance Scores

• loftool: 0.243
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.71

Haploinsufficiency Scores

• pHI: 0.128
• hipred: Y
• hipred_score: 0.605
• ghis: 0.400

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.975

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: E2f7
• Phenotype: normal 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype; respiratory system phenotype; growth/size/body region phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: e2f7
• Affected structure: dorsal longitudinal anastomotic vessel
• Phenotype tag: abnormal
• Phenotype quality: hypoplastic

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;placenta development;sprouting angiogenesis;DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;negative regulation of cell population proliferation;DNA damage response, signal transduction by p53 class mediator;negative regulation of cytokinesis;positive regulation of DNA endoreduplication;positive regulation of transcription by RNA polymerase II;regulation of cell cycle;trophoblast giant cell differentiation;chorionic trophoblast cell differentiation;hepatocyte differentiation;negative regulation of transcription involved in G1/S transition of mitotic cell cycle;negative regulation of G1/S transition of mitotic cell cycle
• Cellular component: nucleus;nucleoplasm;nuclear speck;RNA polymerase II transcription factor complex
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;proximal promoter sequence-specific DNA binding;DNA binding;DNA-binding transcription factor activity;transcription corepressor activity;protein binding;transcription factor binding;identical protein binding;sequence-specific DNA binding