S1PR1

sphingosine-1-phosphate receptor 1, the group of CD molecules|Sphingosine 1-phosphate receptors

Basic information

Region (hg38): 1:101236864-101243713

Previous symbols: [ "EDG1" ]

Links

ENSG00000170989 ∙ NCBI:1901 ∙ OMIM:601974 ∙ HGNC:3165 ∙ Uniprot:P21453 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the S1PR1 gene.

• Inborn genetic diseases (8 variants)
• not provided (2 variants)

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	1
missense			8		1	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	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)
1-101239537-A-G		not specified	Uncertain significance (Apr 25, 2022)
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: gnomAD

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: dbNSFP

• 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