S1PR2
sphingosine-1-phosphate receptor 2, the group of Sphingosine 1-phosphate receptors
Basic information
Region (hg38): 19:10221433-10231331
Previous symbols: [ "EDG5", "DFNB68" ]
Links
Phenotypes
GenCC
Source:
- autosomal recessive nonsyndromic hearing loss 68 (Strong), mode of inheritance: AR
- autosomal recessive nonsyndromic hearing loss 68 (Strong), mode of inheritance: AR
- hearing loss, autosomal recessive (Supportive), mode of inheritance: AR
- nonsyndromic genetic hearing loss (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Deafness, autosomal recessive 68 | AR | Audiologic/Otolaryngologic | Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development | Audiologic/Otolaryngologic | 16703383; 26805784 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (92 variants)
- Inborn_genetic_diseases (44 variants)
- not_specified (15 variants)
- S1PR2-related_disorder (7 variants)
- Autosomal_recessive_nonsyndromic_hearing_loss_68 (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the S1PR2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004230.4. 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 41 | 48 | ||||
| missense | 64 | 76 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 2 | 0 | 65 | 50 | 7 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| S1PR2 | protein_coding | protein_coding | ENST00000590320 | 1 | 7429 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0183 | 0.904 | 125736 | 0 | 10 | 125746 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.53 | 173 | 240 | 0.722 | 0.0000173 | 2217 |
| Missense in Polyphen | 48 | 81.192 | 0.59119 | 852 | ||
| Synonymous | 0.920 | 107 | 120 | 0.893 | 0.00000958 | 815 |
| Loss of Function | 1.49 | 4 | 8.76 | 0.457 | 4.65e-7 | 89 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000529 | 0.0000527 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000653 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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.;
- Disease
- DISEASE: Deafness, autosomal recessive, 68 (DFNB68) [MIM:610419]: A form of non-syndromic sensorineural hearing loss. Sensorineural deafness results from damage to the neural receptors of the inner ear, the nerve pathways to the brain, or the area of the brain that receives sound information. {ECO:0000269|PubMed:26805784}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- 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;Sphingosine 1-phosphate (S1P) pathway;S1P2 pathway
(Consensus)
Recessive Scores
- pRec
- 0.167
Intolerance Scores
- loftool
- 0.137
- rvis_EVS
- -0.4
- rvis_percentile_EVS
- 26.73
Haploinsufficiency Scores
- pHI
- 0.136
- hipred
- N
- hipred_score
- 0.468
- ghis
- 0.488
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.155
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- S1pr2
- Phenotype
- integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; reproductive system 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); pigmentation phenotype; neoplasm; hearing/vestibular/ear 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); immune system phenotype;
Zebrafish Information Network
- Gene name
- s1pr2
- Affected structure
- neuromast hair cell
- Phenotype tag
- abnormal
- Phenotype quality
- apoptotic
Gene ontology
- Biological process
- activation of MAPK activity;sphingosine-1-phosphate receptor signaling pathway;G protein-coupled receptor signaling pathway;positive regulation of cell population proliferation;positive regulation of peptidyl-threonine phosphorylation;actin cytoskeleton reorganization;filopodium assembly;negative regulation of excitatory postsynaptic potential;positive regulation of establishment of endothelial barrier
- Cellular component
- plasma membrane;integral component of membrane
- Molecular function
- G protein-coupled receptor binding;G protein-coupled receptor activity;integrin binding;protein binding;lipid binding;sphingosine-1-phosphate receptor activity