EDEM2

ER degradation enhancing alpha-mannosidase like protein 2, the group of Mannosidases alpha class 1

Basic information

Region (hg38): 20:35115364-35147336

Previous symbols: [ "C20orf49", "C20orf31" ]

Links

ENSG00000088298 ∙ NCBI:55741 ∙ OMIM:610302 ∙ HGNC:15877 ∙ Uniprot:Q9BV94 ∙ 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 EDEM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EDEM2 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					1	1
missense			32	1		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	1	1

Variants in EDEM2

This is a list of pathogenic ClinVar variants found in the EDEM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-35115507-G-A		not specified	Uncertain significance (Aug 05, 2024)
20-35115533-C-T		not specified	Likely benign (Apr 23, 2024)
20-35115578-G-A		not specified	Uncertain significance (Sep 15, 2021)
20-35115579-G-A		not specified	Uncertain significance (Aug 20, 2024)
20-35115584-G-T		not specified	Uncertain significance (Sep 26, 2024)
20-35115585-C-T		not specified	Likely benign (Jun 24, 2022)
20-35115634-C-A		not specified	Uncertain significance (May 29, 2024)
20-35115651-A-C		not specified	Uncertain significance (Jul 19, 2023)
20-35115651-A-T		not specified	Uncertain significance (Jun 29, 2023)
20-35115720-C-T		not specified	Uncertain significance (Aug 02, 2021)
20-35115749-T-C		not specified	Uncertain significance (Jan 04, 2024)
20-35115755-A-G		not specified	Uncertain significance (Mar 20, 2024)
20-35115779-C-T		not specified	Uncertain significance (Oct 24, 2024)
20-35115788-T-C		not specified	Uncertain significance (Sep 29, 2022)
20-35115844-G-C		not specified	Uncertain significance (Apr 24, 2023)
20-35115898-G-A			Benign (Mar 29, 2018)
20-35115899-C-T		Maturity onset diabetes mellitus in young	Uncertain significance (Nov 01, 2019)
20-35115900-G-A		not specified	Uncertain significance (Jun 22, 2023)
20-35118671-G-A		not specified	Uncertain significance (May 18, 2023)
20-35118689-C-T		not specified	Uncertain significance (Dec 28, 2023)
20-35118701-A-G		not specified	Uncertain significance (Aug 26, 2024)
20-35118713-A-G		not specified	Uncertain significance (May 31, 2023)
20-35123913-C-T		not specified	Uncertain significance (Mar 28, 2022)
20-35123920-C-G		not specified	Uncertain significance (Nov 03, 2023)
20-35123938-G-C		not specified	Uncertain significance (Aug 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EDEM2	protein_coding	protein_coding	ENST00000374492	11	162762

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.83e-7	0.995	125663	0	85	125748	0.000338

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	254	333	0.763	0.0000181	3770
Missense in Polyphen		91	144.02	0.63185		1585
Synonymous	0.456	132	139	0.951	0.00000829	1155
Loss of Function	2.51	15	29.7	0.504	0.00000159	313

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000619	0.000619
Ashkenazi Jewish	0.000595	0.000595
East Asian	0.000219	0.000217
Finnish	0.000323	0.000323
European (Non-Finnish)	0.000343	0.000343
Middle Eastern	0.000219	0.000217
South Asian	0.000196	0.000196
Other	0.000815	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the endoplasmic reticulum-associated degradation (ERAD) pathway that targets misfolded glycoproteins for degradation in an N-glycan-dependent manner (PubMed:15537790, PubMed:25092655). May initiate ERAD by promoting the first mannose trimming step of ERAD substrates, from Man9GlcNAc2 to Man8GlcNAc2 (PubMed:25092655). Seems to recognize and bind to exposed hydrophobic regions in target proteins (By similarity). {ECO:0000250|UniProtKB:Q8BJT9, ECO:0000269|PubMed:15537790, ECO:0000269|PubMed:25092655}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);ER Quality Control Compartment (ERQC);Calnexin/calreticulin cycle;Post-translational protein modification;Metabolism of proteins;Asparagine N-linked glycosylation;N-glycan trimming in the ER and Calnexin/Calreticulin cycle (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.888
• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.99

Haploinsufficiency Scores

• pHI: 0.265
• hipred: Y
• hipred_score: 0.614
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.956

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Edem2

Gene ontology

• Biological process: response to unfolded protein;trimming of terminal mannose on B branch;trimming of terminal mannose on C branch;trimming of first mannose on A branch;trimming of second mannose on A branch;ubiquitin-dependent glycoprotein ERAD pathway;positive regulation of retrograde protein transport, ER to cytosol;mannose trimming involved in glycoprotein ERAD pathway
• Cellular component: endoplasmic reticulum;endoplasmic reticulum lumen;membrane;endoplasmic reticulum quality control compartment
• Molecular function: mannosyl-oligosaccharide 1,2-alpha-mannosidase activity;calcium ion binding