S1PR3

sphingosine-1-phosphate receptor 3, the group of Sphingosine 1-phosphate receptors

Basic information

Region (hg38): 9:88990863-89005155

Previous symbols: [ "EDG3", "C9orf47", "C9orf108" ]

Links

ENSG00000213694 ∙ NCBI:1903 ∙ OMIM:601965 ∙ HGNC:3167 ∙ Uniprot:Q99500 ∙ 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 S1PR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S1PR3 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						0
missense			28	2		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	31	2	0

Variants in S1PR3

This is a list of pathogenic ClinVar variants found in the S1PR3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-88991617-G-A		not specified	Uncertain significance (Jul 06, 2021)
9-88991891-C-T		not specified	Uncertain significance (Sep 15, 2021)
9-88991984-A-G		not specified	Uncertain significance (Jul 06, 2021)
9-89001223-G-A		not specified	Uncertain significance (Jun 05, 2024)
9-89001238-G-C		not specified	Likely benign (Apr 12, 2022)
9-89001341-G-C		not specified	Uncertain significance (Feb 23, 2023)
9-89001607-G-A		not specified	Uncertain significance (Oct 12, 2024)
9-89001639-G-A		not specified	Uncertain significance (Sep 17, 2021)
9-89001646-A-G		not specified	Uncertain significance (Sep 25, 2023)
9-89001657-C-T		not specified	Uncertain significance (Mar 15, 2024)
9-89001680-G-T		not specified	Uncertain significance (Feb 28, 2023)
9-89001738-C-T		not specified	Uncertain significance (Jun 05, 2024)
9-89001787-A-T		not specified	Uncertain significance (Dec 06, 2021)
9-89001790-T-C		not specified	Uncertain significance (Mar 28, 2023)
9-89001892-A-G		not specified	Likely benign (Jan 09, 2024)
9-89001904-C-T		not specified	Uncertain significance (Feb 01, 2023)
9-89001909-C-T		not specified	Uncertain significance (May 23, 2024)
9-89002006-G-A		not specified	Uncertain significance (Jun 05, 2024)
9-89002074-G-A		not specified	Uncertain significance (May 15, 2023)
9-89002096-C-T		not specified	Uncertain significance (Jul 12, 2023)
9-89002119-C-T		not specified	Uncertain significance (Jun 17, 2024)
9-89002131-C-G		not specified	Uncertain significance (May 26, 2022)
9-89002161-C-T		not specified	Uncertain significance (Jul 19, 2023)
9-89002162-G-C		not specified	Uncertain significance (Apr 25, 2023)
9-89002164-G-A		not specified	Uncertain significance (Apr 18, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
S1PR3	protein_coding	protein_coding	ENST00000375846	1	13564

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0469	0.864	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.855	198	235	0.843	0.0000149	2480
Missense in Polyphen		75	107.38	0.69846		1176
Synonymous	0.182	103	105	0.978	0.00000720	795
Loss of Function	1.40	3	6.99	0.429	3.05e-7	86

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for the lysosphingolipid sphingosine 1- phosphate (S1P). S1P is a bioactive lysophospholipid that elicits diverse physiological effect on most types of cells and tissues. When expressed in rat HTC4 hepatoma cells, is capable of mediating S1P-induced cell proliferation and suppression of apoptosis. {ECO:0000269|PubMed:10617617}.
• Pathway: Sphingolipid signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Small Ligand GPCRs;Signal Transduction of S1P Receptor;Signaling by GPCR;Signal Transduction;Lysosphingolipid and LPA receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling;S1P3 pathway;Sphingosine 1-phosphate (S1P) pathway (Consensus)

Recessive Scores

• pRec: 0.137

Intolerance Scores

• loftool: 0.396
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.31

Haploinsufficiency Scores

• pHI: 0.124
• hipred: Y
• hipred_score: 0.672
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.647

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: S1pr3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system 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); 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); reproductive system 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); hearing/vestibular/ear phenotype; immune system 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

Gene ontology

• Biological process: cytokine production;sphingosine-1-phosphate receptor signaling pathway;inflammatory response;G protein-coupled receptor signaling pathway;adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway;positive regulation of cytosolic calcium ion concentration;Notch signaling pathway;positive regulation of cell population proliferation;anatomical structure morphogenesis;regulation of interleukin-1 beta production;negative regulation of establishment of endothelial barrier
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: G protein-coupled receptor activity;integrin binding;protein binding;lipid binding;sphingosine-1-phosphate receptor activity