EDEM1
Basic information
Region (hg38): 3:5187646-5219958
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 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:
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:
- 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