Gene Gene information from NCBI Gene database.
Entrez ID 124976
Gene name SPNS lysolipid transporter 2, sphingosine-1-phosphate
Gene symbol SPNS2
Synonyms (NCBI Gene)
DFNB115SLC62A2SLC63A2
Chromosome 17
Chromosome location 17p13.2
Summary The protein encoded by this gene is a transporter of sphingosine 1-phosphate, a secreted lipid that is important in cardiovascular, immunological, and neural development. Defects in this gene are a cause of early onset progressive hearing loss. [provided
SNPs SNP information provided by dbSNP.
2
SNP ID Visualize variation Clinical significance Consequence
rs749994718 TCC>- Pathogenic, uncertain-significance Coding sequence variant, inframe deletion
rs1555537637 CC>T Likely-pathogenic, pathogenic Frameshift variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
189
miRTarBase ID miRNA Experiments Reference
MIRT018966 hsa-miR-335-5p Microarray 18185580
MIRT647400 hsa-miR-8485 HITS-CLIP 23824327
MIRT647401 hsa-miR-7113-5p HITS-CLIP 23824327
MIRT647399 hsa-miR-4685-5p HITS-CLIP 23824327
MIRT647398 hsa-miR-6837-5p HITS-CLIP 23824327
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
34
GO ID Ontology Definition Evidence Reference
GO:0001782 Process B cell homeostasis IEA
GO:0002260 Process Lymphocyte homeostasis IEA
GO:0002920 Process Regulation of humoral immune response IEA
GO:0002920 Process Regulation of humoral immune response ISS
GO:0003376 Process Sphingosine-1-phosphate receptor signaling pathway IBA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
612584 26992 ENSG00000183018
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q8IVW8
Protein name Sphingosine-1-phosphate transporter SPNS2 (Protein spinster homolog 2)
Protein function Lipid transporter that specifically mediates export of sphingosine-1-phosphate (sphing-4-enine 1-phosphate, S1P) and sphinganine-1-phosphate in the lymph, thereby playing a role in lymphocyte trafficking (PubMed:19074308, PubMed:21084291, PubMed
PDB 7YUB , 7YUD , 7YUF , 8EX4 , 8EX5 , 8EX6 , 8EX7 , 8EX8 , 8G92 , 8JHQ , 8JHR , 8KAE , 8QV5 , 8QV6 , 8RL7 , 8RL8 , 8RLC , 8RLD
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF07690 MFS_1 108 476 Major Facilitator Superfamily Family
Sequence
Sequence length 549
Interactions View interactions
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
18
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Hearing loss, autosomal recessive 115 Likely pathogenic rs1555537637 RCV000782132
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Sensorineural hearing loss disorder Likely pathogenic rs1905545130 RCV002281599
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cervical cancer Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Colorectal cancer Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Autoimmune Diseases Autoimmune Diseases BEFREE 30655317
★☆☆☆☆
Found in Text Mining only
Carcinoma of lung Lung carcinoma BEFREE 25330231
★☆☆☆☆
Found in Text Mining only
Cardiac defects Cardiac Defects BEFREE 19074308
★☆☆☆☆
Found in Text Mining only
Colorectal Carcinoma Colorectal Cancer BEFREE 31206801
★☆☆☆☆
Found in Text Mining only
Dysmorphic features Dysmorphic Features CLINVAR_DG 19074308, 25356849, 27899622
★☆☆☆☆
Found in Text Mining only
Glioblastoma Glioblastoma Pubtator 37728571 Inhibit
★☆☆☆☆
Found in Text Mining only
Glioma Glioma Pubtator 37728571 Inhibit
★☆☆☆☆
Found in Text Mining only
Iron Overload Iron Overload BEFREE 29721575
★☆☆☆☆
Found in Text Mining only
Liver Failure Liver failure Pubtator 27562371 Associate
★☆☆☆☆
Found in Text Mining only
Lymphatic Metastasis Lymphatic metastasis Pubtator 33673355 Associate
★☆☆☆☆
Found in Text Mining only