EDEM1

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

Basic information

Region (hg38): 3:5187646-5219958

Links

ENSG00000134109

∙ NCBI:9695 ∙ OMIM:607673 ∙ HGNC:18967 ∙ Uniprot:Q92611 ∙ 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 EDEM1 gene.

not_specified (81 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EDEM1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014674.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			79 clinvar	2 clinvar		81
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	79	2	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EDEM1	protein_coding	protein_coding	ENST00000256497	12	32312

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.06e-13	0.268	125675	0	73	125748	0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.370	327	346	0.944	0.0000179	4218
Missense in Polyphen		115	153.85	0.74747		1790
Synonymous	-1.70	165	139	1.18	0.00000726	1300
Loss of Function	1.17	24	31.0	0.774	0.00000164	358

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000806	0.000804
Ashkenazi Jewish	0.00	0.00
East Asian	0.000652	0.000653
Finnish	0.00	0.00
European (Non-Finnish)	0.000266	0.000255
Middle Eastern	0.000652	0.000653
South Asian	0.000297	0.000294
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Extracts misfolded glycoproteins, but not glycoproteins undergoing productive folding, from the calnexin cycle. It is directly involved in endoplasmic reticulum-associated degradation (ERAD) and targets misfolded glycoproteins for degradation in an N-glycan-independent manner, probably by forming a complex with SEL1L. It has low mannosidase activity, catalyzing mannose trimming from Man8GlcNAc2 to Man7GlcNAc2. {ECO:0000269|PubMed:12610306, ECO:0000269|PubMed:19524542, ECO:0000269|PubMed:19934218, ECO:0000269|PubMed:25092655}.;
Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);XBP1(S) activates chaperone genes;Photodynamic therapy-induced unfolded protein response;er associated degradation (erad) pathway (Consensus)

Recessive Scores

pRec: 0.148

Intolerance Scores

loftool: 0.389
rvis_EVS: -0.96
rvis_percentile_EVS: 9.17

Haploinsufficiency Scores

pHI: 0.383
hipred: Y
hipred_score: 0.771
ghis: 0.634

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.852

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Edem1
Phenotype

Gene ontology

Biological process: ubiquitin-dependent ERAD pathway;IRE1-mediated unfolded protein response;trimming of terminal mannose on C 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;aggresome;integral component of endoplasmic reticulum membrane;endoplasmic reticulum quality control compartment
Molecular function: mannosyl-oligosaccharide 1,2-alpha-mannosidase activity;calcium ion binding;protein binding;misfolded protein binding