S1PR5

protein-coding

sphingosine-1-phosphate receptor 5, the group of Sphingosine 1-phosphate receptors

Gene summary

The lysosphingolipid sphingosine 1-phosphate (S1P) regulates cell proliferation, apoptosis, motility, and neurite retraction. Its actions may be both intracellular as a second messenger and extracellular as a receptor ligand. S1P and the structurally related lysolipid mediator lysophosphatidic acid (LPA) signal cells through a set of G protein-coupled receptors known as EDG receptors. Some EDG receptors (e.g., EDG1; MIM 601974) are S1P receptors; others (e.g., EDG2; MIM 602282) are LPA receptors.[supplied by OMIM, Mar 2008]

Previous symbols:

EDG8

MANE transcript

NM_030760.5

Inheritance

—

ClinVar variants

U:62B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.33

Max pathogenic AF

—

Genomic locus

chr19:10,512,742-10,517,931

External References & Databases

Ensembl (ENSG00000180739)

Transcript & Mutation Effects

hg38 • Region Span ~5.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to S1PR5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 64

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030760.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar	2 clinvar	5
missense			62 clinvar	2 clinvar	1 clinvar	65
nonsense				1 clinvar		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	62	6	3	71

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030760.5	RefSeq	NP_110387.1	1	MANE Select
ENST00000333430.6	Ensembl	ENSP00000328472.3	1	MANE Select
NM_001166215.2	RefSeq	NP_001159687.1	1	Standard
ENST00000439028.3	Ensembl	ENSP00000416915.2	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Sphingolipid signaling pathway - Homo sapiens (human)
Neuroactive ligand-receptor interaction - Homo sapiens (human)
Signal Transduction of S1P Receptor
Signaling by GPCR
Signal Transduction

Biological Process

sphingosine-1-phosphate receptor signaling pathway
G protein-coupled receptor signaling pathway
regulation of neuron differentiation

Molecular Function

sphingosine-1-phosphate receptor activity

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000439028
Coding exons: 1
Length: 4985
Individuals with no LoFs: 125044
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 125052
p: 0.0000320

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.45	199	266	0.749	0.0000166	2392
Missense (PolyPhen)		65	102.58	0.63362		1039
Synonymous	1.34	117	137	0.855	0.00000897	982
Loss of Function	1.53	2	6.08	0.329	2.62e-7	63

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000067	0.000062	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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. Is coupled to both the G(i/0)alpha and G(12) subclass of heteromeric G-proteins (By similarity). May play a regulatory role in the transformation of radial glial cells into astrocytes and may affect proliferative activity of these cells. {ECO:0000250}.;

Recessive Scores

pRec: 0.120

Intolerance Scores

LoFtool: 0.105
RVIS EVS: 0.62
RVIS percentile EVS: 83.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.447

Gene Damage Prediction

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