EDEM1

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

Basic information

Region (hg38): 3:5187646-5219958

Links

ENSG00000134109NCBI:9695OMIM:607673HGNC:18967Uniprot:Q92611AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EDEM1 gene.

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.

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
0
missense
37
clinvar
1
clinvar
38
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 37 1 0

Variants in EDEM1

This is a list of pathogenic ClinVar variants found in the EDEM1 region.

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

Position Type Phenotype Significance ClinVar
3-5187836-G-A not specified Uncertain significance (Jan 24, 2024)2224506
3-5187839-C-T not specified Uncertain significance (Jul 19, 2023)2599830
3-5187977-G-T not specified Uncertain significance (Dec 06, 2022)2224043
3-5187978-G-A not specified Uncertain significance (Dec 02, 2022)2332181
3-5187981-C-T not specified Uncertain significance (Jul 09, 2021)2236165
3-5187983-G-T not specified Uncertain significance (May 08, 2023)2524569
3-5187995-G-C not specified Uncertain significance (Oct 05, 2023)3087157
3-5187998-G-C not specified Uncertain significance (Sep 01, 2021)3087158
3-5188002-T-C not specified Uncertain significance (Feb 16, 2023)2455393
3-5188014-C-T not specified Uncertain significance (Aug 02, 2022)2382312
3-5188026-C-T not specified Uncertain significance (May 13, 2024)3274491
3-5188028-C-T not specified Uncertain significance (Aug 28, 2023)2591126
3-5188043-G-T not specified Uncertain significance (May 30, 2024)3274485
3-5188061-G-C not specified Uncertain significance (Jan 06, 2023)3087159
3-5188098-C-G not specified Uncertain significance (Mar 20, 2024)3274488
3-5188118-G-A not specified Uncertain significance (Oct 26, 2021)2219933
3-5188137-C-G not specified Uncertain significance (Mar 28, 2024)3274490
3-5188163-G-A not specified Uncertain significance (Jun 24, 2022)2297587
3-5188163-G-T not specified Uncertain significance (Jun 16, 2022)2283983
3-5188178-C-A not specified Uncertain significance (Nov 09, 2023)3087160
3-5188206-C-T not specified Uncertain significance (Mar 19, 2024)3274487
3-5188272-A-G not specified Uncertain significance (May 23, 2024)3274492
3-5188301-G-T not specified Uncertain significance (Jan 03, 2024)3087161
3-5199689-C-T not specified Uncertain significance (Nov 10, 2022)2365284
3-5201795-C-G not specified Uncertain significance (Feb 17, 2023)2486685

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
EDEM1protein_codingprotein_codingENST00000256497 1232312
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.06e-130.2681256750731257480.000290
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3703273460.9440.00001794218
Missense in Polyphen115153.850.747471790
Synonymous-1.701651391.180.000007261300
Loss of Function1.172431.00.7740.00000164358

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0008060.000804
Ashkenazi Jewish0.000.00
East Asian0.0006520.000653
Finnish0.000.00
European (Non-Finnish)0.0002660.000255
Middle Eastern0.0006520.000653
South Asian0.0002970.000294
Other0.0003260.000326

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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