SELPLG
protein-codingselectin P ligand, the group of Receptor ligands|CD molecules
Gene summary
This gene encodes a glycoprotein that functions as a high affinity counter-receptor for the cell adhesion molecules P-, E- and L- selectin expressed on myeloid cells and stimulated T lymphocytes. As such, this protein plays a critical role in leukocyte trafficking during inflammation by tethering of leukocytes to activated platelets or endothelia expressing selectins. This protein requires two post-translational modifications, tyrosine sulfation and the addition of the sialyl Lewis x tetrasaccharide (sLex) to its O-linked glycans, for its high-affinity binding activity. Aberrant expression of this gene and polymorphisms in this gene are associated with defects in the innate and adaptive immune response. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Apr 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~13.5 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 SELPLG variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003006.4. 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 | 5 | 1 | 6 | |||
| missense | 53 | 10 | 1 | 64 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 53 | 15 | 2 | 70 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002997.2 | 1 | MANE Select | |
| Ensembl | ENSP00000447752.1 | 1 | MANE Select | |
| RefSeq | NP_001193538.1 | 2 | Standard | |
| Ensembl | ENSP00000228463.6 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Cell adhesion molecules (CAMs) - Homo sapiens (human)
- Staphylococcus aureus infection - Homo sapiens (human)
- Human Complement System
- Cell surface interactions at the vascular wall
- Hemostasis
Biological Process
- cell adhesion
- viral entry into host cell
- leukocyte migration
- leukocyte tethering or rolling
- leukocyte adhesive activation
Molecular Function
- virus receptor activity
- signaling receptor binding
- protein binding
Cellular Component
- uropod
- plasma membrane
- integral component of plasma membrane
- membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000228463
- Coding exons
- 2
- Length
- 12050
- Individuals with no LoFs
- 124325
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 124327
- p
- 0.00000804
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0975 | 246 | 242 | 1.02 | 0.0000136 | 2700 |
| Missense (PolyPhen) | 41 | 48.311 | 0.84868 | 519 | ||
| Synonymous | -1.06 | 116 | 102 | 1.13 | 0.00000622 | 1005 |
| Loss of Function | 0.860 | 1 | 2.45 | 0.408 | 1.04e-7 | 33 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: A SLe(x)-type proteoglycan, which through high affinity, calcium-dependent interactions with E-, P- and L-selectins, mediates rapid rolling of leukocytes over vascular surfaces during the initial steps in inflammation. Critical for the initial leukocyte capture. {ECO:0000269|PubMed:11566773, ECO:0000269|PubMed:12403782}.;
Recessive Scores
- pRec
- 0.132
Intolerance Scores
- LoFtool
- 0.784
- RVIS EVS
- 1.22
- RVIS percentile EVS
- 93.19
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.859
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |