SELL
protein-codingselectin L, the group of C-type lectin domain containing|CD molecules|Sushi domain containing|Selectins
Gene summary
This gene encodes a cell surface adhesion molecule that belongs to a family of adhesion/homing receptors. The encoded protein contains a C-type lectin-like domain, a calcium-binding epidermal growth factor-like domain, and two short complement-like repeats. The gene product is required for binding and subsequent rolling of leucocytes on endothelial cells, facilitating their migration into secondary lymphoid organs and inflammation sites. Single-nucleotide polymorphisms in this gene have been associated with various diseases including immunoglobulin A nephropathy. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Oct 2009]
- LYAM1
- LNHR
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~21.0 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 SELL variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000655.5. 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 | 2 | 2 | ||||
| missense | 49 | 2 | 2 | 53 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 49 | 2 | 4 | 55 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000646.3 | 9 | MANE Select | |
| Ensembl | ENSP00000236147.5 | 9 | MANE Select | |
| Ensembl | ENSP00000498707.1 | 3 | Standard | |
| Ensembl | ENSP00000498227.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Cell adhesion molecules (CAMs) - Homo sapiens (human)
- Human Complement System
- Neutrophil degranulation
- Innate Immune System
- Immune System
Biological Process
- cell adhesion
- calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules
- response to ATP
- neutrophil degranulation
- regulation of immune response
Molecular Function
- protease binding
- calcium ion binding
- protein binding
- heparin binding
- carbohydrate binding
Cellular Component
- plasma membrane
- integral component of plasma membrane
- external side of plasma membrane
- secretory granule membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000236147
- Coding exons
- 9
- Length
- 21032
- Individuals with no LoFs
- 124602
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 17
- Defined
- 124619
- p
- 0.0000682
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.320 | 179 | 191 | 0.935 | 0.00000908 | 2514 |
| Missense (PolyPhen) | 56 | 74.001 | 0.75675 | 959 | ||
| Synonymous | 0.170 | 63 | 64.7 | 0.973 | 0.00000316 | 647 |
| Loss of Function | 1.53 | 13 | 20.5 | 0.635 | 8.64e-7 | 278 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000065 | 0.000065 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000056 | 0.000056 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000085 | 0.000080 | rare |
| South Asian | 0.00023 | 0.00020 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Calcium-dependent lectin that mediates cell adhesion by binding to glycoproteins on neighboring cells (PubMed:12403782, PubMed:28489325, PubMed:28011641). Mediates the adherence of lymphocytes to endothelial cells of high endothelial venules in peripheral lymph nodes. Promotes initial tethering and rolling of leukocytes in endothelia (PubMed:12403782, PubMed:28011641). {ECO:0000269|PubMed:12403782, ECO:0000269|PubMed:28011641, ECO:0000305|PubMed:28489325}.;
Recessive Scores
- pRec
- 0.564
Intolerance Scores
- RVIS EVS
- 0.79
- RVIS percentile EVS
- 87.4
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.871
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |