E2F6

E2F transcription factor 6, the group of E2F transcription factors

Basic information

Region (hg38): 2:11444375-11466177

Links

ENSG00000169016 ∙ NCBI:1876 ∙ OMIM:602944 ∙ HGNC:3120 ∙ Uniprot:O75461 ∙ 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 E2F6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the E2F6 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	18	1	0

Variants in E2F6

This is a list of pathogenic ClinVar variants found in the E2F6 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-11446502-T-G		not specified	Uncertain significance (Jul 26, 2022)
2-11447639-C-G		not specified	Likely benign (Sep 11, 2024)
2-11447653-C-T		not specified	Uncertain significance (Jan 16, 2024)
2-11447672-C-T		not specified	Uncertain significance (Feb 26, 2025)
2-11447743-T-C		not specified	Uncertain significance (Jun 10, 2024)
2-11450047-C-T		not specified	Uncertain significance (Jan 22, 2024)
2-11450056-T-C		not specified	Uncertain significance (Oct 12, 2024)
2-11451740-G-C		not specified	Uncertain significance (Apr 28, 2022)
2-11451790-T-C		not specified	Uncertain significance (Jan 29, 2024)
2-11453565-GTTTGAAAGCAACTCACA-G		Ciliary dyskinesia, primary, 40	Likely pathogenic (Nov 09, 2022)
2-11453622-C-T		not specified	Uncertain significance (Jun 10, 2024)
2-11453639-T-A		not specified	Uncertain significance (Sep 03, 2024)
2-11453639-T-C		not specified	Uncertain significance (Jun 22, 2024)
2-11453666-C-T		not specified	Uncertain significance (Nov 29, 2023)
2-11453681-G-A		not specified	Uncertain significance (Aug 05, 2024)
2-11453723-C-T		not specified	Uncertain significance (Sep 27, 2024)
2-11457191-C-T		not specified	Uncertain significance (Aug 15, 2024)
2-11465773-A-T		not specified	Uncertain significance (Jan 16, 2025)
2-11465788-T-G		not specified	Uncertain significance (Jan 08, 2024)
2-11465794-G-A		not specified	Uncertain significance (Jul 27, 2022)
2-11465807-G-A		not specified	Uncertain significance (Oct 26, 2022)
2-11465863-G-A		not specified	Uncertain significance (Nov 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
E2F6	protein_coding	protein_coding	ENST00000381525	7	21797

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.102	0.892	125723	0	8	125731	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.922	117	149	0.787	0.00000755	1819
Missense in Polyphen		10	33.311	0.3002		445
Synonymous	-0.110	59	57.9	1.02	0.00000318	535
Loss of Function	2.38	4	13.4	0.299	7.16e-7	171

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000463	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibitor of E2F-dependent transcription. Binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC-3'. Has a preference for the 5'-TTTCCCGC-3' E2F recognition site. E2F6 lacks the transcriptional activation and pocket protein binding domains. Appears to regulate a subset of E2F-dependent genes whose products are required for entry into the cell cycle but not for normal cell cycle progression. May silence expression via the recruitment of a chromatin remodeling complex containing histone H3-K9 methyltransferase activity. Overexpression delays the exit of cells from the S-phase.
• Pathway: Cell Cycle;G1 to S cell cycle control;Gene expression (Transcription);Transcriptional Regulation by E2F6;Generic Transcription Pathway;RNA Polymerase II Transcription;E2F transcription factor network (Consensus)

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.334
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.144
• hipred: Y
• hipred_score: 0.831
• ghis: 0.569

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: E2f6
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system 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); reproductive system 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); skeleton phenotype; immune system phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: regulation of transcription involved in G1/S transition of mitotic cell cycle;negative regulation of transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II;regulation of cell cycle;negative regulation of G0 to G1 transition
• Cellular component: nucleus;nucleoplasm;MLL1 complex;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;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;transcription corepressor activity;protein binding;transcription factor binding;sequence-specific DNA binding;protein dimerization activity