EDEM3 ER degradation enhancing alpha-mannosidase like protein 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: EDEM3provided by HGNC
Official Full Name: ER degradation enhancing alpha-mannosidase like protein 3provided by HGNC
Primary source: HGNC:HGNC:16787
See related: Ensembl:ENSG00000116406 MIM:610214; AllianceGenome:HGNC:16787
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: CDG2V; C1orf22
Summary: Quality control in the endoplasmic reticulum (ER) ensures that only properly folded proteins are retained in the cell through recognition and degradation of misfolded or unassembled proteins. EDEM3 belongs to a group of proteins that accelerate degradation of misfolded glycoproteins in the ER (Hirao et al., 2006 [PubMed 16431915]).[supplied by OMIM, Mar 2008]
Expression: Ubiquitous expression in stomach (RPKM 15.9), colon (RPKM 13.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q25.3

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (184690237..184754858, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (184053426..184118046, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (184659371..184723992, complement)

Chromosome 1 - NC_000001.11 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?

Pro-Survival Factor EDEM3 Confers Therapy Resistance in Prostate Cancer.
Title: Pro-Survival Factor EDEM3 Confers Therapy Resistance in Prostate Cancer.
Purified EDEM3 or EDEM1 alone produces determinant oligosaccharide structures from M8B in mammalian glycoprotein ERAD.
Title: Purified EDEM3 or EDEM1 alone produces determinant oligosaccharide structures from M8B in mammalian glycoprotein ERAD.
Bi-allelic variants in the ER quality-control mannosidase gene EDEM3 cause a congenital disorder of glycosylation.
Title: Bi-allelic variants in the ER quality-control mannosidase gene EDEM3 cause a congenital disorder of glycosylation.
EDEM3 Domains Cooperate to Perform Its Overall Cell Functioning.
Title: EDEM3 Domains Cooperate to Perform Its Overall Cell Functioning.
IL8 and EDEM3 gene expression ratio indicates peripheral blood mononuclear cell (PBMC) quality.
Title: IL8 and EDEM3 gene expression ratio indicates peripheral blood mononuclear cell (PBMC) quality.
the mannose-trimming activity of EDEM3 toward the model misfolded substrate, the glycoprotein T-cell receptor alpha locus (TCRalpha), was reconstituted only when ERp46 had established a covalent interaction with EDEM3
Title: ER-resident protein 46 (ERp46) triggers the mannose-trimming activity of ER degradation-enhancing α-mannosidase-like protein 3 (EDEM3).
The data corroborated herein suggest that besides ER residents, EDEM3 interacts also with proteins involved in the ERAD cargo recognition and targeting to degradation translocation into the cytosol, including UBA1 and UBA2 ubiquitinating enzymes. In addition, the results indicate that this network of EDEM3 interactors is highly sensitive to interfering with early ER N-glycan processing.
Title: Inhibition of N-glycan processing modulates the network of EDEM3 interactors.

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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

Associated conditions

Description	Tests
Congenital disorder of glycosylation, type 2v MedGen: C5561971 OMIM: 619493 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
GWAS identifies novel SLE susceptibility genes and explains the association of the HLA region. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. 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)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	HIV-1 gp120 is identified to have a physical interaction with ER degradation enhancer, mannosidase alpha-like 3 (EDEM3) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses	PubMed
Envelope surface glycoprotein gp160, precursor	env	HIV-1 gp160 interacts with EDEM3; predicted interaction to be within the endoplasmic reticulum and function as chaperone for endoplasmic reticulum-associated degradation	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH48990 (e-PCR)
- UniSTS:50718

SHGC-76050 (e-PCR)
- UniSTS:17980

SHGC-53072 (e-PCR)
- UniSTS:67165

SHGC-76042 (e-PCR)
- UniSTS:4310

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables mannosyl-oligosaccharide 1,2-alpha-mannosidase activity	IBA Inferred from Biological aspect of Ancestor more info
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 protein glycosylation	IEA Inferred from Electronic Annotation more info
involved_in ubiquitin-dependent glycoprotein ERAD pathway	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
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 3

Names: ER degradation enhancer, mannosidase alpha-like 3; ER degradation-enhancing -mannosidase-like protein 3; ER degradation-enhancing alpha-mannosidase-like 3; alpha-1,2-mannosidase EDEM3

NP_001306889.1

EC 3.2.1.113

NP_079467.3

EC 3.2.1.113

XP_005245556.1

EC 3.2.1.113

XP_011508314.1

EC 3.2.1.113

XP_054194843.1

EC 3.2.1.113

XP_054194844.1

EC 3.2.1.113

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_001319960.2 → NP_001306889.1 ER degradation-enhancing alpha-mannosidase-like protein 3 isoform 1 precursor

Status: VALIDATED

Description

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

Source sequence(s)

AI521228, AL096819, BC016464, BC144149, DA724785

Consensus CDS

CCDS91128.1

UniProtKB/TrEMBL

A0A8I5KTR7, A0A8J8YX80

Related

ENSP00000356482.4, ENST00000367512.8

Conserved Domains (2) summary

cd02126
Location:664 → 789

PA_EDEM3_like; PA_EDEM3_like: protease associated domain (PA) domain-containing EDEM3-like proteins. This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar ...

pfam01532
Location:59 → 498

Glyco_hydro_47; Glycosyl hydrolase family 47
NM_025191.4 → NP_079467.3 ER degradation-enhancing alpha-mannosidase-like protein 3 isoform 2 precursor

See identical proteins and their annotated locations for NP_079467.3

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AF288393, AI521228, AL096819, BC016464, DA724785

Consensus CDS

CCDS1363.2

UniProtKB/Swiss-Prot

B2RCH6, B7ZLZ2, Q0VGM5, Q5TEZ0, Q7L2Y5, Q9BZQ6, Q9HCW1, Q9UFV7

UniProtKB/TrEMBL

A0A8I5KTR7

Related

ENSP00000318147.7, ENST00000318130.13

Conserved Domains (2) summary

cd02126
Location:664 → 789

PA_EDEM3_like; PA_EDEM3_like: protease associated domain (PA) domain-containing EDEM3-like proteins. This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar ...

pfam01532
Location:59 → 498

Glyco_hydro_47; Glycosyl hydrolase family 47

RNA

NR_135118.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate splice junction compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AI521228, AL096819, BC016464, BC144150, DA724785

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

184690237..184754858 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011510012.2 → XP_011508314.1 ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X2

UniProtKB/TrEMBL

A0A8I5KWI4

Related

ENSP00000509571.1, ENST00000687113.1

Conserved Domains (2) summary

cd02126
Location:588 → 713

PA_EDEM3_like; PA_EDEM3_like: protease associated domain (PA) domain-containing EDEM3-like proteins. This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar ...

pfam01532
Location:1 → 421

Glyco_hydro_47; Glycosyl hydrolase family 47
XM_005245499.3 → XP_005245556.1 ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X1

UniProtKB/TrEMBL

A0A8I5KTR7

Conserved Domains (2) summary

cd02126
Location:665 → 790

PA_EDEM3_like; PA_EDEM3_like: protease associated domain (PA) domain-containing EDEM3-like proteins. This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar ...

pfam01532
Location:59 → 498

Glyco_hydro_47; Glycosyl hydrolase family 47

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

184053426..184118046 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054338869.1 → XP_054194844.1 ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X2

UniProtKB/TrEMBL

A0A8I5KWI4
XM_054338868.1 → XP_054194843.1 ER degradation-enhancing alpha-mannosidase-like protein 3 isoform X1

UniProtKB/TrEMBL

A0A8I5KTR7