EDC4

protein-coding

enhancer of mRNA decapping 4, the group of WD repeat domain containing

Gene summary

Predicted to be involved in deadenylation-independent decapping of nuclear-transcribed mRNA. Located in P-body and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_014329.5

Inheritance

—

ClinVar variants

U:168B:10

Top phenotype

EDC4-related condition

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chr16:67,873,052-67,884,499

External References & Databases

Ensembl (ENSG00000038358)

Transcript & Mutation Effects

hg38 • Region Span ~11.4 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 EDC4 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 158

not providedTotal: 7

EDC4-related conditionTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014329.5. 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			159 clinvar	6 clinvar		165
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	168	9	1	178

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 51 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014329.5	RefSeq	NP_055144.3	29	MANE Select
ENST00000358933.10	Ensembl	ENSP00000351811.5	29	MANE Select
NM_001427345.1	RefSeq	NP_001414274.1	28	Standard
ENST00000573985.5	Ensembl	ENSP00000458357.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

RNA degradation - Homo sapiens (human)
Metabolism of RNA
mRNA decay by 5, to 3, exoribonuclease
Deadenylation-dependent mRNA decay

Biological Process

biological_process
deadenylation-independent decapping of nuclear-transcribed mRNA
exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay

Molecular Function

protein binding

Cellular Component

P-body
nucleus
nucleoplasm
cytoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358933
Coding exons: 29
Length: 11481
Individuals with no LoFs: 125719
Homozygous LoFs: 0
Heterozygous LoFs: 29
Defined: 125748
p: 0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.29	549	813	0.676	0.0000495	9079
Missense (PolyPhen)		128	264.07	0.48471		3005
Synonymous	0.385	316	325	0.973	0.0000187	2910
Loss of Function	5.93	17	70.8	0.240	0.00000390	731

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.000054	0.000054	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0.000098	0.000098	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: In the process of mRNA degradation, seems to play a role in mRNA decapping. Component of a complex containing DCP2 and DCP1A which functions in decapping of ARE-containing mRNAs. Promotes complex formation between DCP1A and DCP2. Enhances the catalytic activity of DCP2 (in vitro). {ECO:0000269|PubMed:16364915}.;

Recessive Scores

pRec: 0.162

Intolerance Scores

LoFtool: 0.0793
RVIS EVS: -1.43
RVIS percentile EVS: 4

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.530

Gene Damage Prediction

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