SEL1L3
protein-codingSEL1L family member 3
Gene summary
Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~116.3 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 SEL1L3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015187.5. 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 | 3 | 1 | 2 | 6 | ||
| missense | 155 | 13 | 5 | 173 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 8 | 8 | ||||
| Total | 0 | 0 | 167 | 14 | 7 | 188 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056002.2 | 24 | MANE Select | |
| Ensembl | ENSP00000382767.3 | 24 | MANE Select | |
| RefSeq | NP_001284521.1 | 24 | Standard | |
| RefSeq | NP_001284523.1 | 23 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Cellular Component
- nucleus
- nucleoplasm
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000399878
- Coding exons
- 24
- Length
- 116328
- Individuals with no LoFs
- 124545
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 96
- Defined
- 124641
- p
- 0.000385
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.30 | 495 | 583 | 0.849 | 0.0000310 | 7333 |
| Missense (PolyPhen) | 138 | 208.3 | 0.6625 | 2577 | ||
| Synonymous | 1.35 | 198 | 224 | 0.885 | 0.0000127 | 2140 |
| Loss of Function | 5.26 | 17 | 61.5 | 0.277 | 0.00000302 | 761 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00092 | 0.00090 | rare |
| Latino/Admixed American | 0.000087 | 0.000087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00017 | 0.00017 | rare |
| Finnish | 0.0023 | 0.0023 | notable |
| European (Non-Finnish) | 0.00019 | 0.00019 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0.00050 | 0.00050 | rare |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.671
- RVIS EVS
- -0.13
- RVIS percentile EVS
- 44.09
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |