ECD

protein-coding

ecdysoneless cell cycle regulator

Gene summary

Enables histone acetyltransferase binding activity. Involved in positive regulation of transcription by RNA polymerase II. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_007265.3

Inheritance

—

ClinVar variants

U:95B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr10:73,130,155-73,169,055

External References & Databases

Ensembl (ENSG00000122882)

Transcript & Mutation Effects

hg38 • Region Span ~38.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ECD variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 78

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007265.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	3 clinvar	1 clinvar	5
missense			83 clinvar	2 clinvar		85
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	95	5	1	101

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007265.3	RefSeq	NP_009196.1	13	MANE Select
ENST00000372979.9	Ensembl	ENSP00000362070.4	13	MANE Select
NM_001135752.1	RefSeq	NP_001129224.1	14	Standard
NM_001135753.1	RefSeq	NP_001129225.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of glycolytic process
transcription by RNA polymerase II
mRNA processing
cell population proliferation
RNA splicing

Molecular Function

transcription coactivator activity
protein binding
histone acetyltransferase binding

Cellular Component

nucleus
nucleoplasm
cytoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000430082
Coding exons: 14
Length: 38901
Individuals with no LoFs: 125620
Homozygous LoFs: 0
Heterozygous LoFs: 128
Defined: 125748
p: 0.000509

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.385	320	340	0.941	0.0000166	4435
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00043	0.00043	rare
Latino/Admixed American	0.00036	0.00035	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00053	0.00049	rare
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.00076	0.00075	rare
South Asian	0.00023	0.00023	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.857

Gene Damage Prediction

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