DERL2
derlin 2, the group of Rhomboid family
Basic information
Region (hg38): 17:5471254-5486811
Links
Phenotypes
GenCC
Source:
No genCC data.
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 DERL2 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 0 |
Variants in DERL2
This is a list of pathogenic ClinVar variants found in the DERL2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-5474719-A-G | not specified | Uncertain significance (Apr 22, 2022) | ||
| 17-5474733-T-C | not specified | Uncertain significance (Jan 23, 2023) | ||
| 17-5474763-T-G | not specified | Uncertain significance (Jun 09, 2022) | ||
| 17-5480096-T-C | not specified | Uncertain significance (Jan 04, 2024) | ||
| 17-5481297-G-A | not specified | Uncertain significance (Jul 20, 2022) | ||
| 17-5486140-G-T | not specified | Uncertain significance (Jan 16, 2024) | ||
| 17-5486148-C-A | not specified | Uncertain significance (Jul 13, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DERL2 | protein_coding | protein_coding | ENST00000158771 | 7 | 15561 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.957 | 0.0426 | 125683 | 0 | 3 | 125686 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.62 | 79 | 131 | 0.603 | 0.00000681 | 1558 |
| Missense in Polyphen | 12 | 32.332 | 0.37115 | 384 | ||
| Synonymous | -1.05 | 56 | 46.9 | 1.20 | 0.00000225 | 456 |
| Loss of Function | 3.26 | 1 | 14.3 | 0.0700 | 9.38e-7 | 150 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Functional component of endoplasmic reticulum-associated degradation (ERAD) for misfolded lumenal glycoproteins, but not that of misfolded nonglycoproteins. May act by forming a channel that allows the retrotranslocation of misfolded glycoproteins into the cytosol where they are ubiquitinated and degraded by the proteasome. May mediate the interaction between VCP and misfolded glycoproteins (PubMed:16186509, PubMed:16449189). May also be involved in endoplasmic reticulum stress-induced pre-emptive quality control, a mechanism that selectively attenuates the translocation of newly synthesized proteins into the endoplasmic reticulum and reroutes them to the cytosol for proteasomal degradation (PubMed:26565908). {ECO:0000269|PubMed:16186509, ECO:0000269|PubMed:16449189, ECO:0000269|PubMed:26565908}.;
- Pathway
- Protein processing in endoplasmic reticulum - Homo sapiens (human);Disorders of transmembrane transporters;Disease;Signal Transduction;Defective CFTR causes cystic fibrosis;ER Quality Control Compartment (ERQC);Calnexin/calreticulin cycle;Post-translational protein modification;Metabolism of proteins;Transport of small molecules;Hedgehog ligand biogenesis;Signaling by Hedgehog;Asparagine N-linked glycosylation;ABC-family proteins mediated transport;N-glycan trimming in the ER and Calnexin/Calreticulin cycle;Hh mutants that don,t undergo autocatalytic processing are degraded by ERAD;Hh mutants abrogate ligand secretion;ABC transporter disorders;Diseases of signal transduction
(Consensus)
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- loftool
- 0.385
- rvis_EVS
- -0.14
- rvis_percentile_EVS
- 42.88
Haploinsufficiency Scores
- pHI
- 0.602
- hipred
- Y
- hipred_score
- 0.775
- ghis
- 0.597
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Derl2
- Phenotype
- reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- suckling behavior;positive regulation of cell population proliferation;positive regulation of cell growth;ubiquitin-dependent ERAD pathway;endoplasmic reticulum unfolded protein response;retrograde protein transport, ER to cytosol;negative regulation of retrograde protein transport, ER to cytosol;endoplasmic reticulum mannose trimming
- Cellular component
- early endosome;late endosome;endoplasmic reticulum;signal recognition particle receptor complex;endoplasmic reticulum membrane;membrane;integral component of endoplasmic reticulum membrane;endoplasmic reticulum quality control compartment;signal recognition particle
- Molecular function
- protein binding