EDEM1

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

Basic information

Region (hg38): 3:5187645-5219958

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.

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	1		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)
3-5187839-C-T		not specified	Uncertain significance (Jul 19, 2023)
3-5187977-G-T		not specified	Uncertain significance (Dec 06, 2022)
3-5187978-G-A		not specified	Uncertain significance (Dec 02, 2022)
3-5187981-C-T		not specified	Uncertain significance (Jul 09, 2021)
3-5187983-G-T		not specified	Uncertain significance (May 08, 2023)
3-5187995-G-C		not specified	Uncertain significance (Oct 05, 2023)
3-5187998-G-C		not specified	Uncertain significance (Sep 01, 2021)
3-5188002-T-C		not specified	Uncertain significance (Feb 16, 2023)
3-5188014-C-T		not specified	Uncertain significance (Aug 02, 2022)
3-5188026-C-T		not specified	Uncertain significance (May 13, 2024)
3-5188028-C-T		not specified	Uncertain significance (Aug 28, 2023)
3-5188043-G-T		not specified	Uncertain significance (May 30, 2024)
3-5188061-G-C		not specified	Uncertain significance (Jan 06, 2023)
3-5188098-C-G		not specified	Uncertain significance (Mar 20, 2024)
3-5188118-G-A		not specified	Uncertain significance (Oct 26, 2021)
3-5188137-C-G		not specified	Uncertain significance (Mar 28, 2024)
3-5188163-G-A		not specified	Uncertain significance (Jun 24, 2022)
3-5188163-G-T		not specified	Uncertain significance (Jun 16, 2022)
3-5188178-C-A		not specified	Uncertain significance (Nov 09, 2023)
3-5188206-C-T		not specified	Uncertain significance (Mar 19, 2024)
3-5188272-A-G		not specified	Uncertain significance (May 23, 2024)
3-5188301-G-T		not specified	Uncertain significance (Jan 03, 2024)
3-5199689-C-T		not specified	Uncertain significance (Nov 10, 2022)
3-5201795-C-G		not specified	Uncertain significance (Feb 17, 2023)

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

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