SEL1L
Basic information
Region (hg38): 14:81471547-81533853
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 SEL1L 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 | 2 | |||||
missense | 37 | 38 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 1 | ||||
non coding | 0 | |||||
Total | 0 | 0 | 37 | 1 | 2 |
Variants in SEL1L
This is a list of pathogenic ClinVar variants found in the SEL1L region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
14-81477025-G-A | not specified | Uncertain significance (Nov 29, 2021) | ||
14-81477034-G-A | not specified | Uncertain significance (Dec 07, 2021) | ||
14-81477180-A-G | not specified | Uncertain significance (May 18, 2022) | ||
14-81479644-C-T | not specified | Uncertain significance (Apr 22, 2022) | ||
14-81484307-C-T | not specified | Uncertain significance (Nov 10, 2022) | ||
14-81485681-C-T | not specified | Uncertain significance (Apr 08, 2024) | ||
14-81485699-G-C | not specified | Uncertain significance (Jul 19, 2022) | ||
14-81485718-T-G | not specified | Uncertain significance (May 27, 2022) | ||
14-81485723-T-C | not specified | Uncertain significance (Feb 05, 2024) | ||
14-81486316-T-C | not specified | Uncertain significance (Dec 20, 2021) | ||
14-81486357-T-C | not specified | Uncertain significance (Apr 07, 2023) | ||
14-81486379-C-A | not specified | Uncertain significance (Apr 11, 2023) | ||
14-81486385-C-T | not specified | Uncertain significance (Jan 26, 2023) | ||
14-81486427-G-A | not specified | Uncertain significance (Sep 26, 2023) | ||
14-81489256-T-C | not specified | Uncertain significance (Jun 02, 2023) | ||
14-81489277-T-C | not specified | Uncertain significance (Sep 29, 2023) | ||
14-81492529-T-C | not specified | Uncertain significance (May 13, 2022) | ||
14-81492533-A-G | not specified | Uncertain significance (Feb 27, 2024) | ||
14-81498470-C-T | not specified | Uncertain significance (May 05, 2022) | ||
14-81499465-C-T | not specified | Uncertain significance (Jun 16, 2023) | ||
14-81499512-C-T | not specified | Uncertain significance (Feb 27, 2024) | ||
14-81502813-G-C | not specified | Uncertain significance (Feb 03, 2022) | ||
14-81502839-T-C | not specified | Uncertain significance (Oct 10, 2023) | ||
14-81502876-G-A | not specified | Uncertain significance (Sep 30, 2021) | ||
14-81504204-C-T | not specified | Uncertain significance (Aug 12, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SEL1L | protein_coding | protein_coding | ENST00000336735 | 21 | 62313 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.982 | 0.0177 | 125730 | 0 | 17 | 125747 | 0.0000676 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.41 | 289 | 430 | 0.672 | 0.0000218 | 5191 |
Missense in Polyphen | 84 | 167.27 | 0.50218 | 1968 | ||
Synonymous | 0.156 | 153 | 155 | 0.984 | 0.00000794 | 1484 |
Loss of Function | 5.32 | 8 | 47.6 | 0.168 | 0.00000228 | 584 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000280 | 0.000275 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000887 | 0.0000879 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000675 | 0.0000653 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role in the endoplasmic reticulum quality control (ERQC) system also called ER-associated degradation (ERAD) involved in ubiquitin-dependent degradation of misfolded endoplasmic reticulum proteins (PubMed:16186509). Enhances SYVN1 stability. Plays a role in LPL maturation and secretion. Required for normal differentiation of the pancreas epithelium, and for normal exocrine function and survival of pancreatic cells. May play a role in Notch signaling. {ECO:0000250|UniProtKB:Q9Z2G6, ECO:0000269|PubMed:16186509}.;
- 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
- 0.186
Intolerance Scores
- loftool
- 0.492
- rvis_EVS
- 0.15
- rvis_percentile_EVS
- 64.74
Haploinsufficiency Scores
- pHI
- 0.366
- hipred
- Y
- hipred_score
- 0.756
- ghis
- 0.430
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.952
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sel1l
- Phenotype
- growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; skeleton phenotype; digestive/alimentary phenotype;
Zebrafish Information Network
- Gene name
- sel1l
- Affected structure
- post-vent vasculature
- Phenotype tag
- abnormal
- Phenotype quality
- hemorrhagic
Gene ontology
- Biological process
- triglyceride metabolic process;Notch signaling pathway;protein secretion;ubiquitin-dependent ERAD pathway;retrograde protein transport, ER to cytosol;ERAD pathway;protein stabilization;transmembrane transport;endoplasmic reticulum mannose trimming
- Cellular component
- Hrd1p ubiquitin ligase complex;Hrd1p ubiquitin ligase ERAD-L complex;endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane;Derlin-1 retrotranslocation complex;endoplasmic reticulum quality control compartment
- Molecular function
- protein binding