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.

• not_specified (53 variants)

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. These statistics are base on transcript: NM_000005226.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			49	2		51
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	49	2	0

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	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

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

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