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

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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.

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				3	2	5
missense			22	1	1	24
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	5	3

Variants in S1PR5

This is a list of pathogenic ClinVar variants found in the S1PR5 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-10513832-C-T		not specified	Uncertain significance (Aug 02, 2021)
19-10513834-G-C			Likely benign (Jul 16, 2018)
19-10513905-C-G		not specified	Uncertain significance (May 26, 2024)
19-10513939-C-T		not specified	Uncertain significance (Jun 30, 2023)
19-10514017-G-A		not specified	Likely benign (Jun 18, 2021)
19-10514028-G-A			Likely benign (May 01, 2022)
19-10514089-A-T			Benign (Jul 16, 2018)
19-10514110-A-G		not specified	Uncertain significance (Sep 14, 2022)
19-10514182-C-A		not specified	Uncertain significance (Dec 19, 2023)
19-10514187-C-T			Benign (Jul 23, 2018)
19-10514192-C-A		not specified	Uncertain significance (Jul 14, 2021)
19-10514309-T-C		not specified	Uncertain significance (May 15, 2024)
19-10514326-C-T		not specified	Uncertain significance (Mar 01, 2023)
19-10514329-G-A		not specified	Uncertain significance (Dec 26, 2023)
19-10514368-A-C		not specified	Uncertain significance (Dec 21, 2022)
19-10514381-G-C		not specified	Uncertain significance (Sep 28, 2022)
19-10514414-C-G		not specified	Uncertain significance (Nov 28, 2023)
19-10514445-G-A			Benign (Jun 14, 2018)
19-10514476-A-G		not specified	Uncertain significance (Oct 13, 2023)
19-10514504-C-A		not specified	Uncertain significance (Jun 07, 2024)
19-10514563-C-A		not specified	Uncertain significance (Sep 17, 2021)
19-10514583-C-T			Likely benign (May 17, 2018)
19-10514585-C-T		not specified	Uncertain significance (Jan 04, 2022)
19-10514589-C-T			Benign/Likely benign (May 01, 2022)
19-10514627-T-C		not specified	Uncertain significance (Feb 21, 2024)

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
0.157	0.782	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

Haploinsufficiency Scores

• pHI: 0.0946
• hipred: N
• hipred_score: 0.438

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

Mouse Genome Informatics

• Gene name: S1pr5
• 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); hematopoietic system phenotype; immune system phenotype

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