S1PR5

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

Basic information

Region (hg38): 19:10512742-10517931

Previous symbols: [ "EDG8" ]

Links

ENSG00000180739 ∙ NCBI:53637 ∙ OMIM:605146 ∙ HGNC:14299 ∙ Uniprot:Q9H228 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 5.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_030760.5	NP_110387.1	1	yes	-
ENST00000333430.6	ENSP00000328472.3	1	yes	-
NM_001166215.2	NP_001159687.1	1	-	-
ENST00000439028.3	ENSP00000416915.2	1	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the S1PR5 gene.

• not_specified (64 variants)
• not_provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S1PR5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_030760.5. 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				3	2	5
missense			62	2	1	65
nonsense				1		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	62	6	3

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
S1PR5	protein_coding	protein_coding	ENST00000439028	1	4985

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125044	0	8	125052	0.0000320

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.45	199	266	0.749	0.0000166	2392
Missense in 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

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	0.0000472	0.0000462
European (Non-Finnish)	0.0000675	0.0000621
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. 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}.
• Pathway: Sphingolipid signaling pathway - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Signal Transduction of S1P Receptor;Signaling by GPCR;Signal Transduction;Lysosphingolipid and LPA receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;S1P5 pathway;G alpha (i) signalling events;GPCR downstream signalling;S1P4 pathway;Sphingosine 1-phosphate (S1P) pathway (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.105
• rvis_EVS: 0.62
• rvis_percentile_EVS: 83.25

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.447

Gene Damage Prediction

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

Gene ontology

• Biological process: sphingosine-1-phosphate receptor signaling pathway;G protein-coupled receptor signaling pathway;regulation of neuron differentiation
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: sphingosine-1-phosphate receptor activity