EP400

E1A binding protein p400, the group of Tip60/Nua4 histone acetyltransferase complex subunits|Myb/SANT domain containing|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 12:131949942-132080460

Previous symbols: [ "TNRC12" ]

Links

ENSG00000183495 ∙ NCBI:57634 ∙ OMIM:606265 ∙ HGNC:11958 ∙ Uniprot:Q96L91 ∙ 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 EP400 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EP400 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				69	21	90
missense			186	33	7	226
nonsense			5			5
start loss						0
frameshift			4	1		5
inframe indel				1	7	8
splice donor/acceptor (+/-2bp)			2			2
splice region			1	4	3	8
non coding				4	3	7
Total	0	0	197	108	38

Variants in EP400

This is a list of pathogenic ClinVar variants found in the EP400 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-131960613-G-A		EP400-related disorder	Benign (Aug 30, 2019)
12-131960615-T-C		EP400-related disorder	Likely benign (Mar 10, 2020)
12-131960622-G-C		EP400-related disorder	Uncertain significance (May 28, 2024)
12-131960631-C-A		EP400-related disorder	Likely benign (Jul 23, 2019)
12-131960676-C-A		EP400-related disorder	Likely benign (Jun 11, 2019)
12-131960678-G-T		not specified	Likely benign (Mar 07, 2023)
12-131960689-G-A		not specified	Uncertain significance (Sep 27, 2022)
12-131960709-C-G		EP400-related disorder	Likely benign (Apr 25, 2019)
12-131960711-A-C		EP400-related disorder	Benign (Apr 25, 2019)
12-131960721-A-C		EP400-related disorder	Likely benign (Apr 13, 2020)
12-131960742-C-T		EP400-related disorder	Likely benign (Aug 25, 2023)
12-131960746-G-A		not specified	Uncertain significance (Apr 01, 2024)
12-131960752-T-C		EP400-related disorder	Uncertain significance (Aug 15, 2023)
12-131960766-G-A			Likely benign (Apr 01, 2023)
12-131960807-A-G		not specified	Likely benign (Dec 21, 2023)
12-131960853-C-T			Benign (Aug 16, 2018)
12-131960868-C-G			Likely benign (May 01, 2023)
12-131960876-A-G			Benign (Apr 01, 2024)
12-131960888-C-T		not specified	Uncertain significance (Aug 04, 2023)
12-131960903-C-T		not specified	Uncertain significance (Mar 06, 2023)
12-131960938-A-G		not specified	Uncertain significance (Dec 16, 2023)
12-131960991-G-A			Benign (Jul 26, 2018)
12-131961041-C-T		not specified	Uncertain significance (Dec 28, 2023)
12-131961057-C-T			Likely benign (Jul 20, 2018)
12-131961071-G-A		not specified	Uncertain significance (Feb 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EP400	protein_coding	protein_coding	ENST00000389561	52	130498

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.84e-9	125606	7	135	125748	0.000565

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.56	1535	1.84e+3	0.832	0.000121	20033
Missense in Polyphen		78	145.77	0.53509		1465
Synonymous	-2.32	905	820	1.10	0.0000606	6528
Loss of Function	9.90	23	157	0.147	0.00000812	1626

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00220	0.00200
Ashkenazi Jewish	0.000906	0.000794
East Asian	0.000170	0.000163
Finnish	0.000286	0.000277
European (Non-Finnish)	0.000388	0.000343
Middle Eastern	0.000170	0.000163
South Asian	0.00134	0.00131
Other	0.000493	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of select genes principally by acetylation of nucleosomal histones H4 and H2A. This modification may both alter nucleosome - DNA interactions and promote interaction of the modified histones with other proteins which positively regulate transcription. May be required for transcriptional activation of E2F1 and MYC target genes during cellular proliferation. The NuA4 complex ATPase and helicase activities seem to be, at least in part, contributed by the association of RUVBL1 and RUVBL2 with EP400. May regulate ZNF42 transcription activity. Component of a SWR1-like complex that specifically mediates the removal of histone H2A.Z/H2AFZ from the nucleosome. {ECO:0000269|PubMed:14966270, ECO:0000269|PubMed:24463511}.
• Pathway: Formation of Senescence-Associated Heterochromatin Foci (SAHF);DNA Damage/Telomere Stress Induced Senescence;Cellular Senescence;Cellular responses to stress;Chromatin modifying enzymes;HATs acetylate histones;Cellular responses to external stimuli;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.279

Intolerance Scores

• loftool: 0.00889
• rvis_EVS: -3.86
• rvis_percentile_EVS: 0.22

Haploinsufficiency Scores

• pHI: 0.186
• hipred: Y
• hipred_score: 0.652
• ghis: 0.633

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.976

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ep400
• 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); 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); hematopoietic system phenotype; embryo phenotype

Gene ontology

• Biological process: histone H4 acetylation;histone H2A acetylation
• Cellular component: Swr1 complex;nucleoplasm;nuclear speck;NuA4 histone acetyltransferase complex
• Molecular function: DNA binding;chromatin binding;helicase activity;protein binding;ATP binding;protein antigen binding