S1PR1
sphingosine-1-phosphate receptor 1, the group of CD molecules|Sphingosine 1-phosphate receptors
Basic information
Region (hg38): 1:101236865-101243713
Previous symbols: [ "EDG1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the S1PR1 gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 10 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 0 | 2 |
Variants in S1PR1
This is a list of pathogenic ClinVar variants found in the S1PR1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-101239016-C-A | Benign (Jun 13, 2018) | |||
| 1-101239028-C-T | not specified | Uncertain significance (Dec 20, 2023) | ||
| 1-101239176-C-G | not specified | Uncertain significance (Feb 22, 2023) | ||
| 1-101239313-A-T | not specified | Uncertain significance (May 22, 2023) | ||
| 1-101239414-A-G | not specified | Uncertain significance (Aug 28, 2023) | ||
| 1-101239444-G-A | not specified | Uncertain significance (Dec 02, 2024) | ||
| 1-101239537-A-G | not specified | Uncertain significance (Apr 25, 2022) | ||
| 1-101239631-C-G | not specified | Uncertain significance (May 30, 2024) | ||
| 1-101239635-C-T | Benign (May 24, 2018) | |||
| 1-101239703-A-G | not specified | Uncertain significance (Dec 06, 2022) | ||
| 1-101239984-G-A | not specified | Uncertain significance (May 08, 2023) | ||
| 1-101239988-A-G | not specified | Uncertain significance (Apr 06, 2023) | ||
| 1-101240016-C-G | not specified | Uncertain significance (Feb 10, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| S1PR1 | protein_coding | protein_coding | ENST00000305352 | 1 | 4631 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.733 | 0.265 | 125683 | 0 | 2 | 125685 | 0.00000796 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.61 | 120 | 232 | 0.518 | 0.0000157 | 2487 |
| Missense in Polyphen | 19 | 78.035 | 0.24348 | 883 | ||
| Synonymous | -0.177 | 106 | 104 | 1.02 | 0.00000737 | 818 |
| Loss of Function | 2.42 | 1 | 8.68 | 0.115 | 5.45e-7 | 107 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.000199 | 0.0000993 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000884 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: G-protein coupled receptor for the bioactive lysosphingolipid sphingosine 1-phosphate (S1P) that seems to be coupled to the G(i) subclass of heteromeric G proteins. Signaling leads to the activation of RAC1, SRC, PTK2/FAK1 and MAP kinases. Plays an important role in cell migration, probably via its role in the reorganization of the actin cytoskeleton and the formation of lamellipodia in response to stimuli that increase the activity of the sphingosine kinase SPHK1. Required for normal chemotaxis toward sphingosine 1-phosphate. Required for normal embryonic heart development and normal cardiac morphogenesis. Plays an important role in the regulation of sprouting angiogenesis and vascular maturation. Inhibits sprouting angiogenesis to prevent excessive sprouting during blood vessel development. Required for normal egress of mature T-cells from the thymus into the blood stream and into peripheral lymphoid organs. Plays a role in the migration of osteoclast precursor cells, the regulation of bone mineralization and bone homeostasis (By similarity). Plays a role in responses to oxidized 1-palmitoyl-2-arachidonoyl-sn-glycero-3- phosphocholine by pulmonary endothelial cells and in the protection against ventilator-induced lung injury. {ECO:0000250, ECO:0000269|PubMed:10982820, ECO:0000269|PubMed:11230698, ECO:0000269|PubMed:11583630, ECO:0000269|PubMed:11604399, ECO:0000269|PubMed:19286607, ECO:0000269|PubMed:22344443, ECO:0000269|PubMed:8626678, ECO:0000269|PubMed:9488656}.;
- Pathway
- FoxO signaling pathway - Homo sapiens (human);Sphingolipid signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);GPCRs, Other;Small Ligand GPCRs;Signal Transduction of S1P Receptor;Interleukin-4 and 13 signaling;Signaling by GPCR;Signal Transduction;phospholipids as signalling intermediaries;Lysosphingolipid and LPA receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling;Fc-epsilon receptor I signaling in mast cells;S1P1 pathway;PDGFR-beta signaling pathway;Sphingosine 1-phosphate (S1P) pathway
(Consensus)
Recessive Scores
- pRec
- 0.184
Intolerance Scores
- loftool
- 0.0757
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58.53
Haploinsufficiency Scores
- pHI
- 0.301
- hipred
- Y
- hipred_score
- 0.680
- ghis
- 0.501
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.773
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- S1pr1
- Phenotype
- muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; immune system phenotype; embryo phenotype; normal phenotype; 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); 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); hematopoietic system phenotype; vision/eye phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- s1pr1
- Affected structure
- nucleate erythrocyte
- Phenotype tag
- abnormal
- Phenotype quality
- increased accumulation
Gene ontology
- Biological process
- angiogenesis;blood vessel maturation;cardiac muscle tissue growth involved in heart morphogenesis;sphingosine-1-phosphate receptor signaling pathway;chemotaxis;cell adhesion;G protein-coupled receptor signaling pathway;adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway;brain development;cell migration;cytokine-mediated signaling pathway;transmission of nerve impulse;lamellipodium assembly;regulation of cell adhesion;neuron differentiation;positive regulation of cell migration;regulation of bone mineralization;leukocyte chemotaxis;actin cytoskeleton reorganization;positive regulation of GTPase activity;regulation of bone resorption;endothelial cell differentiation;positive regulation of transcription by RNA polymerase II;positive regulation of smooth muscle cell proliferation;positive regulation of positive chemotaxis;positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G protein-coupled signaling pathway;negative regulation of stress fiber assembly;heart trabecula morphogenesis;T cell migration
- Cellular component
- nucleoplasm;endosome;plasma membrane;external side of plasma membrane;integral component of membrane;intrinsic component of plasma membrane;intracellular membrane-bounded organelle;membrane raft
- Molecular function
- G protein-coupled receptor binding;G protein-coupled receptor activity;protein binding;sphingosine-1-phosphate receptor activity;sphingolipid binding