ECD

ecdysoneless cell cycle regulator

Basic information

Region (hg38): 10:73130155-73169055

Links

ENSG00000122882 ∙ NCBI:11319 ∙ OMIM:616464 ∙ HGNC:17029 ∙ Uniprot:O95905 ∙ 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 ECD gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ECD 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				3	1	4
missense			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	24	5	1

Variants in ECD

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

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

Position	Type	Phenotype	Significance	ClinVar
10-73130704-T-C		not specified	Uncertain significance (Nov 28, 2024)
10-73130719-G-C		not specified	Uncertain significance (May 03, 2023)
10-73130720-A-C		not specified	Uncertain significance (Aug 01, 2022)
10-73130769-C-G		not specified	Uncertain significance (Jun 25, 2024)
10-73130845-C-T		not specified	Uncertain significance (Sep 15, 2021)
10-73130879-G-C		not specified	Uncertain significance (Dec 21, 2022)
10-73130895-C-A		not specified	Uncertain significance (Oct 27, 2023)
10-73134727-G-T		not specified	Uncertain significance (Jul 14, 2021)
10-73134731-A-G		not specified	Uncertain significance (May 23, 2023)
10-73134746-A-C		not specified	Uncertain significance (Nov 09, 2023)
10-73134809-G-A		not specified	Uncertain significance (Sep 25, 2024)
10-73134822-T-C			Likely benign (Jul 16, 2018)
10-73136789-T-A		not specified	Uncertain significance (Sep 10, 2024)
10-73136897-T-G		not specified	Uncertain significance (Sep 30, 2021)
10-73138054-G-A		not specified	Uncertain significance (Aug 08, 2023)
10-73139347-T-C		not specified	Uncertain significance (Dec 06, 2021)
10-73139410-G-A			Benign (Dec 31, 2019)
10-73139424-A-G		not specified	Likely benign (Feb 03, 2022)
10-73139428-T-G		not specified	Uncertain significance (Dec 26, 2023)
10-73139444-T-A		not specified	Uncertain significance (Oct 22, 2021)
10-73139653-T-C			Likely benign (Jul 06, 2018)
10-73139676-T-C		not specified	Uncertain significance (Apr 04, 2023)
10-73139722-G-T		not specified	Uncertain significance (Dec 07, 2024)
10-73146361-C-T		not specified	Uncertain significance (Jun 26, 2024)
10-73148331-G-A		not specified	Uncertain significance (Oct 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ECD	protein_coding	protein_coding	ENST00000430082	14	38901

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.34e-12	0.855	125620	0	128	125748	0.000509

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.385	320	340	0.941	0.0000166	4435
Missense in Polyphen		97	120.91	0.80225		1619
Synonymous	0.546	115	123	0.937	0.00000600	1268
Loss of Function	1.88	24	36.2	0.663	0.00000212	426

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000791	0.000789
Ashkenazi Jewish	0.00	0.00
East Asian	0.000530	0.000489
Finnish	0.000234	0.000231
European (Non-Finnish)	0.000763	0.000747
Middle Eastern	0.000530	0.000489
South Asian	0.000233	0.000229
Other	0.000501	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator of p53/TP53 stability and function. Inhibits MDM2-mediated degradation of p53/TP53 possibly by cooperating in part with TXNIP (PubMed:16849563, PubMed:23880345). May be involved transcriptional regulation. In vitro has intrinsic transactivation activity enhanced by EP300. May be a transcriptional activator required for the expression of glycolytic genes (PubMed:19919181, PubMed:9928932). Involved in regulation of cell cycle progression. Proposed to disrupt Rb-E2F binding leading to transcriptional activation of E2F proteins (PubMed:19640839). The cell cycle -regulating function may depend on its RUVBL1-mediated association with the R2TP complex (PubMed:26711270). May play a role in regulation of pre-mRNA splicing (PubMed:24722212). {ECO:0000269|PubMed:16849563, ECO:0000269|PubMed:19640839, ECO:0000269|PubMed:19919181, ECO:0000269|PubMed:23880345, ECO:0000269|PubMed:26711270, ECO:0000305|PubMed:24722212, ECO:0000305|PubMed:9928932}.

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.998
• rvis_EVS: 0.05
• rvis_percentile_EVS: 57.52

Haploinsufficiency Scores

• pHI: 0.189
• hipred: N
• hipred_score: 0.144
• ghis: 0.535

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.857

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ecd
• 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)

Gene ontology

• Biological process: regulation of glycolytic process;transcription by RNA polymerase II;mRNA processing;cell population proliferation;RNA splicing;positive regulation of transcription by RNA polymerase II;regulation of G1/S transition of mitotic cell cycle
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol
• Molecular function: transcription coactivator activity;protein binding;histone acetyltransferase binding