EDC4

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

Basic information

Region (hg38): 16:67873052-67884499

Links

ENSG00000038358 ∙ NCBI:23644 ∙ OMIM:606030 ∙ HGNC:17157 ∙ Uniprot:Q6P2E9 ∙ 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 EDC4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EDC4 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				2	1	3
missense			53			53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					1	1
Total	0	0	53	2	2

Variants in EDC4

This is a list of pathogenic ClinVar variants found in the EDC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-67873338-C-G		not specified	Uncertain significance (Mar 31, 2022)
16-67875960-G-T		not specified	Uncertain significance (May 06, 2022)
16-67875965-C-T		not specified	Uncertain significance (May 05, 2023)
16-67875975-G-T		not specified	Uncertain significance (Dec 19, 2023)
16-67875984-A-G		not specified	Uncertain significance (Aug 01, 2024)
16-67875996-A-G		not specified	Uncertain significance (Jul 23, 2024)
16-67876092-A-G		not specified	Uncertain significance (Apr 20, 2023)
16-67876559-G-A		not specified	Uncertain significance (Mar 01, 2024)
16-67877354-G-A		not specified	Uncertain significance (Jun 17, 2024)
16-67877378-C-T		not specified	Uncertain significance (Jun 13, 2022)
16-67877655-G-A		not specified	Uncertain significance (Aug 01, 2024)
16-67877766-T-A		not specified	Uncertain significance (May 17, 2023)
16-67877774-A-G			Likely benign (Jun 01, 2024)
16-67877792-G-A		not specified	Uncertain significance (Feb 03, 2022)
16-67877798-G-A		not specified	Uncertain significance (Aug 08, 2023)
16-67877822-A-G		not specified	Uncertain significance (Jan 26, 2023)
16-67878198-G-A			Benign (Mar 30, 2018)
16-67878223-G-A		not specified	Uncertain significance (Oct 26, 2022)
16-67878224-A-G		not specified	Uncertain significance (Nov 28, 2024)
16-67878265-G-A		not specified	Uncertain significance (Jan 05, 2022)
16-67878550-G-A		not specified	Uncertain significance (Sep 09, 2024)
16-67878748-A-G		not specified	Uncertain significance (Sep 08, 2024)
16-67879080-C-T		not specified	Uncertain significance (Aug 19, 2024)
16-67879238-T-G		not specified	Likely benign (Aug 15, 2024)
16-67879319-T-G			Benign (Jun 06, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EDC4	protein_coding	protein_coding	ENST00000358933	29	11481

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.106	0.894	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.29	549	813	0.676	0.0000495	9079
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000243	0.000242
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

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}.
• Pathway: RNA degradation - Homo sapiens (human);Metabolism of RNA;mRNA decay by 5, to 3, exoribonuclease;Deadenylation-dependent mRNA decay (Consensus)

Recessive Scores

• pRec: 0.162

Intolerance Scores

• loftool: 0.0793
• rvis_EVS: -1.43
• rvis_percentile_EVS: 4

Haploinsufficiency Scores

• pHI: 0.301
• hipred: Y
• hipred_score: 0.622
• ghis: 0.598

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.530

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Edc4
• Phenotype: immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms 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

Gene ontology

• Biological process: biological_process;deadenylation-independent decapping of nuclear-transcribed mRNA;exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay
• Cellular component: P-body;nucleus;nucleoplasm;cytoplasm;cytosol;membrane;cytoplasmic ribonucleoprotein granule
• Molecular function: protein binding