EDC3

enhancer of mRNA decapping 3

Basic information

Region (hg38): 15:74630557-74696292

Previous symbols: [ "YJDC" ]

Links

ENSG00000179151 ∙ NCBI:80153 ∙ OMIM:609842 ∙ HGNC:26114 ∙ Uniprot:Q96F86 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal recessive non-syndromic intellectual disability (Supportive), mode of inheritance: AR
• intellectual disability, autosomal recessive 50 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, autosomal recessive 50	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	25701870

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EDC3 gene.

• not provided (13 variants)
• Inborn genetic diseases (13 variants)
• not specified (1 variants)
• Intellectual disability, autosomal recessive 50 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EDC3 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				9		9
missense			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	13	10	0

Variants in EDC3

This is a list of pathogenic ClinVar variants found in the EDC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-74632618-A-G			Likely benign (Jul 10, 2018)
15-74632708-G-A			Likely benign (Mar 01, 2023)
15-74632729-G-A			Likely benign (Jul 16, 2018)
15-74632750-C-T		EDC3-related disorder	Likely benign (Nov 12, 2019)
15-74632764-G-A			Likely benign (Jun 14, 2018)
15-74635417-C-T		not specified	Uncertain significance (Jul 25, 2023)
15-74635432-C-G		not specified	Uncertain significance (Jun 06, 2023)
15-74635499-G-T		not specified	Conflicting classifications of pathogenicity (Nov 07, 2022)
15-74640487-G-T		not specified	Uncertain significance (Dec 05, 2022)
15-74640491-G-A			Likely benign (Sep 01, 2022)
15-74640506-C-T		not specified	Uncertain significance (Mar 07, 2023)
15-74640563-C-T		not specified	Uncertain significance (Dec 16, 2023)
15-74640577-T-C		not specified	Uncertain significance (Feb 13, 2024)
15-74640579-A-T		not specified	Uncertain significance (Feb 13, 2024)
15-74640608-C-A		not specified	Uncertain significance (Dec 02, 2021)
15-74655734-C-T			Benign (Dec 31, 2019)
15-74655735-G-A		not specified	Uncertain significance (Dec 27, 2023)
15-74655775-G-A		Intellectual disability, autosomal recessive 50	Uncertain significance (Jan 22, 2021)
15-74655825-C-T		not specified	Uncertain significance (Feb 15, 2023)
15-74655828-G-C		not specified	Uncertain significance (Feb 23, 2023)
15-74655858-C-T		not specified	Uncertain significance (Aug 20, 2023)
15-74655920-A-C		EDC3-related disorder	Benign/Likely benign (Dec 31, 2019)
15-74655977-G-A			Likely benign (Apr 01, 2023)
15-74656039-C-G		not specified	Uncertain significance (Mar 29, 2022)
15-74656040-CT-C		Intellectual disability, autosomal recessive 50	Pathogenic (Apr 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EDC3	protein_coding	protein_coding	ENST00000315127	6	65735

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0260	0.972	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.05	191	289	0.661	0.0000164	3356
Missense in Polyphen		46	91.944	0.5003		1111
Synonymous	0.948	101	114	0.887	0.00000649	1023
Loss of Function	2.67	6	18.3	0.327	8.53e-7	218

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000123
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000551	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000886	0.0000879
Middle Eastern	0.0000551	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds single-stranded RNA. Involved in the process of mRNA degradation and in the positive regulation of mRNA decapping. May play a role in spermiogenesis and oogenesis. {ECO:0000269|PubMed:16364915, ECO:0000269|PubMed:17533573, ECO:0000269|PubMed:18678652, ECO:0000269|PubMed:25701870}.
• Disease: DISEASE: Mental retardation, autosomal recessive 50 (MRT50) [MIM:616460]: A form of mental retardation, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRT50 patients show mild intellectual disability and microcephaly. {ECO:0000269|PubMed:25701870}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: RNA degradation - Homo sapiens (human);Metabolism of RNA;mRNA decay by 5, to 3, exoribonuclease;Deadenylation-dependent mRNA decay (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.138
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.35

Haploinsufficiency Scores

• pHI: 0.630
• hipred: Y
• hipred_score: 0.786
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.843

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Edc3

Gene ontology

• Biological process: deadenylation-independent decapping of nuclear-transcribed mRNA;cytoplasmic mRNA processing body assembly;exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay;RNA phosphodiester bond hydrolysis, endonucleolytic
• Cellular component: P-body;cytosol;membrane;cytoplasmic ribonucleoprotein granule
• Molecular function: mRNA binding;protein binding;identical protein binding;phosphodiesterase decapping endonuclease activity