SELP
selectin P, the group of CD molecules|Sushi domain containing|Selectins|C-type lectin domain containing
Basic information
Region (hg38): 1:169588849-169630193
Previous symbols: [ "GRMP" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (90 variants)
- not_provided (15 variants)
- SELECTIN_P_POLYMORPHISM (1 variants)
- Premature_coronary_artery_atherosclerosis (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SELP gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003005.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 5 | |||||
| missense | 89 | 99 | ||||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 1 | 90 | 9 | 6 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SELP | protein_coding | protein_coding | ENST00000263686 | 16 | 41345 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 5.04e-32 | 0.0000172 | 125156 | 4 | 588 | 125748 | 0.00236 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.256 | 474 | 459 | 1.03 | 0.0000239 | 5425 |
| Missense in Polyphen | 160 | 157.49 | 1.016 | 1910 | ||
| Synonymous | -0.668 | 185 | 174 | 1.06 | 0.00000989 | 1564 |
| Loss of Function | -0.215 | 47 | 45.4 | 1.03 | 0.00000209 | 544 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00165 | 0.00165 |
| Ashkenazi Jewish | 0.0000995 | 0.0000992 |
| East Asian | 0.000446 | 0.000435 |
| Finnish | 0.0122 | 0.0122 |
| European (Non-Finnish) | 0.00160 | 0.00159 |
| Middle Eastern | 0.000446 | 0.000435 |
| South Asian | 0.00401 | 0.00278 |
| Other | 0.00263 | 0.00245 |
dbNSFP
Source:
- Function
- FUNCTION: Ca(2+)-dependent receptor for myeloid cells that binds to carbohydrates on neutrophils and monocytes. Mediates the interaction of activated endothelial cells or platelets with leukocytes. The ligand recognized is sialyl-Lewis X. Mediates rapid rolling of leukocyte rolling over vascular surfaces during the initial steps in inflammation through interaction with SELPLG. {ECO:0000269|PubMed:11081633, ECO:0000269|PubMed:28011641, ECO:0000269|PubMed:7585950}.;
- Pathway
- Cell adhesion molecules (CAMs) - Homo sapiens (human);Malaria - Homo sapiens (human);Staphylococcus aureus infection - Homo sapiens (human);Spinal Cord Injury;Human Complement System;Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Cell surface interactions at the vascular wall;Hemostasis;amb2 Integrin signaling;IL4-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.530
Intolerance Scores
- loftool
- 0.937
- rvis_EVS
- 1.01
- rvis_percentile_EVS
- 90.81
Haploinsufficiency Scores
- pHI
- 0.0586
- hipred
- N
- hipred_score
- 0.146
- ghis
- 0.423
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.537
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Selp
- Phenotype
- growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; vision/eye phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); respiratory system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; skeleton phenotype; renal/urinary system phenotype;
Zebrafish Information Network
- Gene name
- selp
- Affected structure
- intermediate cell mass of mesoderm
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- platelet degranulation;positive regulation of leukocyte migration;inflammatory response;cell adhesion;heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;leukocyte cell-cell adhesion;positive regulation of platelet activation;positive regulation of phosphatidylinositol 3-kinase signaling;calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules;response to lipopolysaccharide;regulation of integrin activation;calcium-mediated signaling using intracellular calcium source;defense response to Gram-negative bacterium;leukocyte migration;leukocyte tethering or rolling
- Cellular component
- extracellular space;plasma membrane;integral component of plasma membrane;external side of plasma membrane;platelet dense granule membrane;platelet alpha granule membrane
- Molecular function
- lipopolysaccharide binding;calcium ion binding;protein binding;heparin binding;sialic acid binding;fucose binding;glycosphingolipid binding;calcium-dependent protein binding;oligosaccharide binding