E2F2

E2F transcription factor 2, the group of E2F transcription factors

Basic information

Region (hg38): 1:23506438-23531233

Links

ENSG00000007968 ∙ NCBI:1870 ∙ OMIM:600426 ∙ HGNC:3114 ∙ Uniprot:Q14209 ∙ 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 E2F2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the E2F2 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			23	1	1	25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	3	1

Variants in E2F2

This is a list of pathogenic ClinVar variants found in the E2F2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-23509923-T-C		not specified	Uncertain significance (Aug 02, 2021)
1-23509986-A-C		not specified	Uncertain significance (Jun 16, 2024)
1-23510010-G-A		not specified	Uncertain significance (Jun 06, 2022)
1-23510059-G-A		not specified	Uncertain significance (Oct 18, 2021)
1-23510125-G-C		not specified	Uncertain significance (Aug 15, 2023)
1-23510127-G-A		not specified	Uncertain significance (Aug 02, 2021)
1-23516346-G-A		not specified	Uncertain significance (Nov 22, 2023)
1-23516446-T-G		not specified	Uncertain significance (Aug 01, 2022)
1-23516451-G-A			Benign (Jun 08, 2018)
1-23516461-C-T		not specified	Uncertain significance (Jan 27, 2022)
1-23516486-G-A			Likely benign (Jun 01, 2018)
1-23516493-C-T		not specified	Uncertain significance (Aug 04, 2023)
1-23516526-T-C		not specified	Uncertain significance (Mar 18, 2024)
1-23519071-A-G		not specified	Uncertain significance (Nov 12, 2021)
1-23519073-T-C			Likely benign (Jun 01, 2018)
1-23520914-T-C		not specified	Uncertain significance (Feb 14, 2024)
1-23520982-G-A		not specified	Uncertain significance (May 23, 2023)
1-23521034-T-C		not specified	Uncertain significance (Jun 16, 2024)
1-23521045-G-A			Likely benign (Jun 08, 2018)
1-23521955-C-T		not specified	Uncertain significance (Dec 08, 2023)
1-23521976-C-T		not specified	Uncertain significance (Mar 17, 2023)
1-23524391-C-A		not specified	Uncertain significance (May 26, 2022)
1-23524446-C-T		not specified	Uncertain significance (Jul 13, 2022)
1-23524449-C-T		not specified	Uncertain significance (Jul 14, 2021)
1-23524460-A-G		not specified	Uncertain significance (Sep 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
E2F2	protein_coding	protein_coding	ENST00000361729	7	24791

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.255	0.744	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.997	196	239	0.819	0.0000130	2777
Missense in Polyphen		55	82.529	0.66644		973
Synonymous	-0.903	128	116	1.11	0.00000700	920
Loss of Function	2.83	4	16.3	0.245	6.95e-7	196

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000751	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.000134	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription activator that binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC- 3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The DRTF1/E2F complex functions in the control of cell-cycle progression from g1 to s phase. E2F2 binds specifically to RB1 in a cell-cycle dependent manner.
• Pathway: Non-small cell lung cancer - Homo sapiens (human);Chronic myeloid leukemia - Homo sapiens (human);Gastric cancer - Homo sapiens (human);Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Melanoma - Homo sapiens (human);Cushing,s syndrome - Homo sapiens (human);Bladder cancer - Homo sapiens (human);Cell cycle - Homo sapiens (human);Small cell lung cancer - Homo sapiens (human);Breast cancer - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Glioma - Homo sapiens (human);Prostate cancer - Homo sapiens (human);MicroRNAs in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Hepatitis B - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Pancreatic cancer - Homo sapiens (human);Cell Cycle;Retinoblastoma (RB) in Cancer;Hepatitis C and Hepatocellular Carcinoma;G1 to S cell cycle control;Oncogene Induced Senescence;Oxidative Stress Induced Senescence;Cellular Senescence;Cellular responses to stress;Cyclin D associated events in G1;G1 Phase;Mitotic G1-G1/S phases;Cellular responses to external stimuli;Direct p53 effectors;Cell Cycle;Cell Cycle, Mitotic;Regulation of retinoblastoma protein;E2F transcription factor network (Consensus)

Recessive Scores

• pRec: 0.195

Intolerance Scores

• loftool: 0.119
• rvis_EVS: 1.22
• rvis_percentile_EVS: 93.16

Haploinsufficiency Scores

• pHI: 0.355
• hipred: Y
• hipred_score: 0.771
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.873

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: E2f2
• Phenotype: respiratory system phenotype; liver/biliary system phenotype; hematopoietic system 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); normal phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); renal/urinary system phenotype; immune system phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region 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)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;transcription initiation from RNA polymerase II promoter;cell cycle;positive regulation of transcription by RNA polymerase II;regulation of cell cycle;intrinsic apoptotic signaling pathway by p53 class mediator;negative regulation of sprouting angiogenesis;lens fiber cell apoptotic process
• Cellular component: nucleus;nucleoplasm;RNA polymerase II transcription factor complex
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;proximal promoter sequence-specific DNA binding;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding;transcription factor binding;sequence-specific DNA binding;protein dimerization activity