EDEM2 ER degradation enhancing alpha-mannosidase like protein 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: EDEM2provided by HGNC
Official Full Name: ER degradation enhancing alpha-mannosidase like protein 2provided by HGNC
Primary source: HGNC:HGNC:15877
See related: Ensembl:ENSG00000088298 MIM:610302; AllianceGenome:HGNC:15877
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: C20orf31; C20orf49; bA4204.1
Summary: In the endoplasmic reticulum (ER), misfolded proteins are retrotranslocated to the cytosol and degraded by the proteasome in a process known as ER-associated degradation (ERAD). EDEM2 belongs to a family of proteins involved in ERAD of glycoproteins (Mast et al., 2005 [PubMed 15537790]).[supplied by OMIM, Mar 2008]
Expression: Ubiquitous expression in placenta (RPKM 13.1), lung (RPKM 12.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 20q11.22

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (35115364..35147336, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (36836129..36868105, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (33703167..33735139, complement)

Chromosome 20 - NC_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

EDEM2 stably disulfide-bonded to TXNDC11 catalyzes the first mannose trimming step in mammalian glycoprotein ERAD.
Title: EDEM2 stably disulfide-bonded to TXNDC11 catalyzes the first mannose trimming step in mammalian glycoprotein ERAD.
A novel gene in early childhood diabetes: EDEM2 silencing decreases SLC2A2 and PXD1 expression, leading to impaired insulin secretion.
Title: A novel gene in early childhood diabetes: EDEM2 silencing decreases SLC2A2 and PXD1 expression, leading to impaired insulin secretion.
EDEM2 and OS-9 are required for ER-associated degradation of non-glycosylated sonic hedgehog
Title: EDEM2 and OS-9 are required for ER-associated degradation of non-glycosylated sonic hedgehog.
Glycoproteins mannose trimming from Man9GlcNAc2 to Man8GlcNAc2 is conducted mainly by EDEM2.
Title: EDEM2 initiates mammalian glycoprotein ERAD by catalyzing the first mannose trimming step.
Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: Genome-wide association study identifies novel loci for plasma levels of protein C: the ARIC study.
Overexpression of EDEM2 accelerates the degradation of misfolded alpha1-antitrypsin, indicating that the protein is involved in endoplasmic reticulum associated degradation.
Title: Human EDEM2, a novel homolog of family 47 glycosidases, is involved in ER-associated degradation of glycoproteins.
EDEM2 regulates endoplasmic reticulum-associated glycoprotein degradation
Title: A novel stress-induced EDEM variant regulating endoplasmic reticulum-associated glycoprotein degradation.
Degrades misfolded alpha1-antitrypsin in the ER.
Title: Human EDEM2, a novel homolog of family 47 glycosidases, is involved in ER-associated degradation of glycoproteins.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genetic associations for activated partial thromboplastin time and prothrombin time, their gene expression profiles, and risk of coronary artery disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome wide association study for plasma levels of natural anticoagulant inhibitors and protein C anticoagulant pathway: the MARTHA project. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study identifies novel loci for plasma levels of protein C: the ARIC study. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Readthrough MMP24-AS1-EDEM2

Readthrough gene: MMP24-AS1-EDEM2, Included gene: MMP24OS

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
NOT enables mannosyl-oligosaccharide 1,2-alpha-mannosidase activity	IDA Inferred from Direct Assay more info	PubMed
enables mannosyl-oligosaccharide 1,2-alpha-mannosidase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables mannosyl-oligosaccharide 1,2-alpha-mannosidase activity	TAS Traceable Author Statement more info

Process	Evidence Code	Pubs
involved_in ERAD pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in carbohydrate metabolic process	IEA Inferred from Electronic Annotation more info
involved_in endoplasmic reticulum mannose trimming	IEA Inferred from Electronic Annotation more info
involved_in endoplasmic reticulum unfolded protein response	IBA Inferred from Biological aspect of Ancestor more info
involved_in mannoprotein catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in mannoprotein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of retrograde protein transport, ER to cytosol	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of retrograde protein transport, ER to cytosol	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ubiquitin-dependent glycoprotein ERAD pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in viral protein processing	TAS Traceable Author Statement more info

Component	Evidence Code	Pubs
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in endoplasmic reticulum lumen	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum quality control compartment	TAS Traceable Author Statement more info
located_in membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: ER degradation-enhancing alpha-mannosidase-like protein 2

Names: ER degradation enhancer, mannosidase alpha-like 2; ER degradation-enhancing alpha-mannosidase-like 2; ER degradation-enhancing-mannosidase-like protein 2

NP_001138497.1

EC 3.2.1.-

NP_060687.2

EC 3.2.1.-

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001145025.2 → NP_001138497.1 ER degradation-enhancing alpha-mannosidase-like protein 2 isoform 2 precursor

See identical proteins and their annotated locations for NP_001138497.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an exon in the 5' coding region compared to variant 1 although maintains the reading frame. The encoded protein (isoform 2) is shorter but has the same N- and C-termini compared to isoform 1.

Source sequence(s)

AY358580, BP297100, BU188881

Consensus CDS

CCDS46592.1

UniProtKB/TrEMBL

B4DQG9

Related

ENSP00000363615.2, ENST00000374491.3

Conserved Domains (1) summary

pfam01532
Location:36 → 443

Glyco_hydro_47; Glycosyl hydrolase family 47
NM_018217.3 → NP_060687.2 ER degradation-enhancing alpha-mannosidase-like protein 2 isoform 1 precursor

See identical proteins and their annotated locations for NP_060687.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

BC001371, BP297100, BU188881

Consensus CDS

CCDS13247.1

UniProtKB/Swiss-Prot

B4DTG9, Q6GU33, Q6IA89, Q6UWZ4, Q9BV94, Q9H4U0, Q9H886, Q9NTL9, Q9NVE6

UniProtKB/TrEMBL

B4DQG9

Related

ENSP00000363616.3, ENST00000374492.8

Conserved Domains (1) summary

pfam01532
Location:42 → 480

Glyco_hydro_47; Glycosyl hydrolase family 47

RNA

NR_026728.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks the alternate splicing in the 5' coding region observed in variant 1. This variant is represented as non-coding because the use of the expected translational start codon as used in variant 1 renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK298794, AL356652, BU188881