S1PR4

sphingosine-1-phosphate receptor 4, the group of Sphingosine 1-phosphate receptors

Basic information

Region (hg38): 19:3172346-3180332

Previous symbols: [ "EDG6" ]

Links

ENSG00000125910 ∙ NCBI:8698 ∙ OMIM:603751 ∙ HGNC:3170 ∙ Uniprot:O95977 ∙ 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 S1PR4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S1PR4 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				5	1	6
missense			51	3		54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	51	8	1

Variants in S1PR4

This is a list of pathogenic ClinVar variants found in the S1PR4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-3178804-G-A			Likely benign (Mar 01, 2023)
19-3178827-C-T		not specified	Uncertain significance (Oct 20, 2024)
19-3178842-C-T		not specified	Uncertain significance (Feb 12, 2025)
19-3178847-G-A		not specified	Likely benign (Jun 16, 2023)
19-3178860-G-A		not specified	Uncertain significance (Jan 10, 2023)
19-3178878-A-G		not specified	Uncertain significance (Jun 06, 2023)
19-3178901-G-A		not specified	Uncertain significance (Jan 24, 2025)
19-3178904-C-T		not specified	Uncertain significance (Sep 01, 2024)
19-3178940-C-T		not specified	Uncertain significance (Aug 01, 2024)
19-3178941-G-A		not specified	Uncertain significance (Dec 20, 2022)
19-3178950-C-T		not specified	Uncertain significance (Jan 30, 2024)
19-3178958-G-A		not specified	Uncertain significance (Nov 24, 2024)
19-3179007-C-A		not specified	Uncertain significance (Oct 26, 2022)
19-3179025-G-A		not specified	Uncertain significance (May 10, 2023)
19-3179028-G-A		not specified	Uncertain significance (Oct 19, 2024)
19-3179053-C-G		not specified	Uncertain significance (Jul 30, 2024)
19-3179053-C-T			Likely benign (Jun 01, 2022)
19-3179077-G-A			Benign/Likely benign (Mar 01, 2023)
19-3179081-G-A		not specified	Uncertain significance (Dec 16, 2024)
19-3179083-G-A			Likely benign (Jun 01, 2022)
19-3179093-G-A		not specified	Uncertain significance (Jul 20, 2021)
19-3179106-T-C		not specified	Uncertain significance (Nov 09, 2021)
19-3179127-G-A		not specified	Uncertain significance (Aug 30, 2022)
19-3179137-C-T			Likely benign (Mar 01, 2023)
19-3179138-G-A		not specified	Uncertain significance (Feb 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
S1PR4	protein_coding	protein_coding	ENST00000246115	1	7986

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00238	0.787	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0789	262	266	0.986	0.0000201	2385
Missense in Polyphen		72	89.253	0.8067		971
Synonymous	-1.77	152	127	1.20	0.00000924	909
Loss of Function	1.01	5	8.09	0.618	4.29e-7	77

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. May be involved in cell migration processes that are specific for lymphocytes. {ECO:0000269|PubMed:10679247, ECO:0000269|PubMed:10753843}.
• Pathway: FoxO signaling pathway - Homo sapiens (human);Sphingolipid signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Small Ligand GPCRs;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;S1P4 pathway;Sphingosine 1-phosphate (S1P) pathway (Consensus)

Recessive Scores

• pRec: 0.146

Intolerance Scores

• loftool: 0.0607
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.78

Haploinsufficiency Scores

• pHI: 0.141
• hipred: Y
• hipred_score: 0.542
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.938

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: S1pr4
• 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); hematopoietic system 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: s1pr4
• Affected structure: neutrophil
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: sphingosine-1-phosphate receptor signaling pathway;immune response;G protein-coupled receptor signaling pathway;adenylate cyclase-activating G protein-coupled receptor signaling pathway;activation of phospholipase C activity;positive regulation of cytosolic calcium ion concentration
• Cellular component: mitochondrion;plasma membrane;integral component of plasma membrane
• Molecular function: G protein-coupled receptor activity;lipid binding;sphingosine-1-phosphate receptor activity