SEL1L2
protein-codingSEL1L2 adaptor subunit of ERAD E3 ubiquitin ligase
Gene summary
Predicted to be involved in ERAD pathway. Located in cilium and nuclear speck. [provided by Alliance of Genome Resources, Jul 2025]
- C20orf50
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~147.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SEL1L2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_025229.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | 2 | |||
| missense | 1 | 1 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 3 | 1 | 0 | 4 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_079505.1 | 20 | MANE Select | |
| Ensembl | ENSP00000284951.5 | 20 | MANE Select | |
| RefSeq | NP_001258468.1 | 18 | Standard | |
| RefSeq | NP_001350681.1 | 14 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Protein processing in endoplasmic reticulum - Homo sapiens (human)
Cellular Component
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000378072
- Coding exons
- 18
- Length
- 147197
- Individuals with no LoFs
- 124698
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 98
- Defined
- 124796
- p
- 0.000393
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.267 | 279 | 292 | 0.956 | 0.0000144 | 3756 |
| Missense (PolyPhen) | 102 | 116.5 | 0.87551 | 1514 | ||
| Synonymous | 0.924 | 98 | 110 | 0.888 | 0.00000636 | 1016 |
| Loss of Function | 0.670 | 32 | 36.4 | 0.880 | 0.00000169 | 484 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00070 | 0.00065 | rare |
| Latino/Admixed American | 0.00026 | 0.00023 | rare |
| Ashkenazi Jewish | 0.00030 | 0.00030 | rare |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00039 | 0.00039 | rare |
| South Asian | 0.00086 | 0.00085 | rare |
| Other | 0.00055 | 0.00050 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0744
Intolerance Scores
- RVIS EVS
- 0.42
- RVIS percentile EVS
- 77.23
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0353
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |