EID3

EP300 interacting inhibitor of differentiation 3

Basic information

Region (hg38): 12:104303738-104305205

Links

ENSG00000255150 ∙ NCBI:493861 ∙ OMIM:612986 ∙ HGNC:32961 ∙ Uniprot:Q8N140 ∙ 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 EID3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EID3 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			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	0

Variants in EID3

This is a list of pathogenic ClinVar variants found in the EID3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-104303941-A-G		not specified	Likely benign (Mar 06, 2023)
12-104303959-G-C		not specified	Uncertain significance (Sep 13, 2023)
12-104303965-G-A		not specified	Uncertain significance (Mar 28, 2023)
12-104303966-G-A		not specified	Uncertain significance (Aug 02, 2023)
12-104303981-T-G		not specified	Uncertain significance (Dec 19, 2022)
12-104304035-A-G		not specified	Uncertain significance (Oct 30, 2023)
12-104304077-T-G		not specified	Uncertain significance (Jan 02, 2024)
12-104304148-G-A		not specified	Uncertain significance (Dec 28, 2023)
12-104304149-A-T		not specified	Uncertain significance (Dec 28, 2023)
12-104304189-A-T		not specified	Uncertain significance (Jan 02, 2024)
12-104304203-C-T		not specified	Uncertain significance (Jun 13, 2023)
12-104304273-C-A		not specified	Uncertain significance (Dec 18, 2023)
12-104304277-A-G		not specified	Uncertain significance (Mar 20, 2024)
12-104304295-G-T		not specified	Uncertain significance (Sep 01, 2021)
12-104304299-T-C		not specified	Uncertain significance (Mar 21, 2024)
12-104304360-T-G		not specified	Uncertain significance (Mar 15, 2024)
12-104304466-G-C		not specified	Uncertain significance (Apr 22, 2024)
12-104304515-A-G		not specified	Uncertain significance (May 05, 2022)
12-104304572-A-T		not specified	Uncertain significance (Feb 11, 2022)
12-104304692-C-A		not specified	Uncertain significance (Dec 27, 2023)
12-104304730-G-T		not specified	Uncertain significance (Jul 29, 2023)
12-104304814-G-A		not specified	Uncertain significance (Feb 26, 2024)
12-104304876-G-T		not specified	Uncertain significance (Dec 16, 2023)
12-104304883-A-G		not specified	Uncertain significance (Mar 04, 2024)
12-104304886-G-C		not specified	Uncertain significance (Mar 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EID3	protein_coding	protein_coding	ENST00000527879	1	1464

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.408	0.585	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.108	199	195	1.02	0.0000113	2218
Missense in Polyphen		49	59.402	0.82489		682
Synonymous	0.798	66	74.8	0.883	0.00000464	624
Loss of Function	2.24	2	9.40	0.213	6.39e-7	106

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Tissue-specific component of the SMC5-SMC6 complex, a complex involved in repair of DNA double-strand breaks by homologous recombination. The complex may promote sister chromatid homologous recombination by recruiting the SMC1-SMC3 cohesin complex to double-strand breaks. The complex is required for telomere maintenance via recombination and mediates sumoylation of shelterin complex (telosome) components. {ECO:0000269|PubMed:15987788}.
• Pathway: SUMOylation of DNA damage response and repair proteins;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;Metabolism of proteins;SUMOylation (Consensus)

Intolerance Scores

• loftool: 0.763
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.26

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.132
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Eid3

Gene ontology

• Biological process: DNA repair;DNA recombination;positive regulation of response to DNA damage stimulus
• Cellular component: chromosome, telomeric region;nucleus;nucleoplasm;nucleolus;cytoplasm;Smc5-Smc6 complex
• Molecular function: protein binding