SGPP1

Summary

SGPP1 (sphingosine-1-phosphate phosphatase 1, HGNC:17720) is a protein-coding gene on chromosome 14q23.2, encoding Sphingosine-1-phosphate phosphatase 1 (Q9BX95). Specifically dephosphorylates sphingosine 1-phosphate (S1P), dihydro-S1P, and phyto-S1P.

Sphingosine-1-phosphate (S1P) is a bioactive sphingolipid metabolite that regulates diverse biologic processes. SGPP1 catalyzes the degradation of S1P via salvage and recycling of sphingosine into long-chain ceramides (Mandala et al., 2000 [PubMed 10859351]; Le Stunff et al., 2007 [PubMed 17895250]).

Source: NCBI Gene 81537 — RefSeq curated summary.

At a glance

• GWAS associations: 51
• Clinical variants (ClinVar): 68 total
• MANE Select transcript: NM_030791

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17720
Approved symbol	SGPP1
Name	sphingosine-1-phosphate phosphatase 1
Location	14q23.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000126821
Ensembl biotype	protein_coding
OMIM	612826
Entrez	81537

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000247225, ENST00000855967

RefSeq mRNA: 1 — MANE Select: NM_030791 NM_030791

CCDS: CCDS9760

Canonical transcript exons

ENST00000247225 — 3 exons

Exon	Start	End
ENSE00003992971	63727261	63728065
ENSE00003992972	63684216	63686656
ENSE00003992973	63698569	63698658

Expression profiles

Bgee: expression breadth ubiquitous, 135 present calls, max score 89.38.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.7996 / max 217.6806, expressed in 1785 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
143606	17.5914	1783
143607	0.2082	57

Top tissues by expression

135 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
lymph node	UBERON:0000029	89.38	gold quality
placenta	UBERON:0001987	89.24	gold quality
islet of Langerhans	UBERON:0000006	88.56	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	86.59	gold quality
endometrium	UBERON:0001295	85.68	gold quality
adult mammalian kidney	UBERON:0000082	84.99	gold quality
pancreas	UBERON:0001264	84.91	gold quality
right lobe of liver	UBERON:0001114	84.86	gold quality
Brodmann (1909) area 9	UBERON:0013540	84.75	gold quality
calcaneal tendon	UBERON:0003701	84.63	gold quality
prefrontal cortex	UBERON:0000451	84.51	gold quality
superior frontal gyrus	UBERON:0002661	84.49	gold quality
corpus callosum	UBERON:0002336	83.93	gold quality
leukocyte	CL:0000738	83.71	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	83.51	gold quality
monocyte	CL:0000576	83.48	gold quality
kidney	UBERON:0002113	83.48	gold quality
vermiform appendix	UBERON:0001154	83.42	gold quality
body of pancreas	UBERON:0001150	83.38	gold quality
cortex of kidney	UBERON:0001225	83.32	gold quality
left adrenal gland	UBERON:0001234	83.31	gold quality
smooth muscle tissue	UBERON:0001135	83.21	gold quality
right adrenal gland cortex	UBERON:0035827	83.16	gold quality
gall bladder	UBERON:0002110	83.02	gold quality
rectum	UBERON:0001052	83.01	gold quality
left adrenal gland cortex	UBERON:0035825	82.83	gold quality
stromal cell of endometrium	CL:0002255	82.74	gold quality
liver	UBERON:0002107	82.69	gold quality
adrenal gland	UBERON:0002369	82.69	gold quality
substantia nigra	UBERON:0002038	82.66	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-CURD-119	yes	24.65
E-ANND-3	no	1.35

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NR1I2

miRNA regulators (miRDB)

176 targeting SGPP1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-27A-3P	99.98	72.13	2955

Literature-anchored findings (GeneRIF, showing 14)

• sphingosine-1-phosphate phosphatase 1 plays roles in the regulation of intra- and extracellular sphingosine-1-phosphate levels and cell viability (PMID:12815058)
• sphingosine-1-phosphate phosphatase 1 has a role in epidermal growth factor-induced chemotaxis (PMID:15180992)
• SPP-1 regulates ceramide levels in the ER and thus influences the anterograde membrane transport of both ceramide and proteins from the ER to the Golgi apparatus. (PMID:16782891)
• Sphingosine kinase 2, but not sphingosine kinase 1, acted in concert with SPP-1 to regulate recycling of sphingosine into ceramide. (PMID:17895250)
• SPP1 by regulating intracellular S1P homeostasis, can control the UPR and ER stress-induced autophagy. (PMID:20798685)
• Under normal circumstances, the retinal vascular pericytes maintain pericyte-endothelial contacts and vascular barrier function through the secretion of sphingosine 1-phosphate. (PMID:21940944)
• doxorubicin switches protective autophagy in SPP1-depleted cells to apoptosis by calpain-mediated Atg5 cleavage. (PMID:22052905)
• S1P is elevated in patients with IPF, correlates with the lung function and mediates EMT. (PMID:22106015)
• The sphingolipid phosphatase SGPP1, an antagonist of sphingosine-1-phosphate signaling, is a target of miR-95 that promotes radiation resistance. (PMID:24145350)
• Study has revealed miR-27a as a tumor suppressor and has identified SGPP1 and Smad2 as novel targets of miR-27a, linking to STAT3 for regulating cancer cell proliferation, apoptosis and migration in colorectal cancer. (PMID:25166914)
• The two gastric cancer cells transfected with pEF-SGPP1 exhibited a slower rate of growth with less adhesion. Thus, our findings provided evidence that SGPP1 may serve as a prognostic biomarker for patients with advanced gastric cancers. (PMID:26239167)
• the sequential expression and localization of the endogenous S1P regulators SGPP-1 and SGPL-1 and highlight their contribution to the sphingolipid rheostat in inflammation. (PMID:29375197)
• Sevoflurane suppresses cell viability and invasion and promotes cell apoptosis in colon cancer by modulating exosomemediated circHMGCS1 via the miR34a5p/SGPP1 axis. (PMID:33125091)
• MicroRNA-656-3p inhibits colorectal cancer cell migration, invasion, and chemo-resistance by targeting sphingosine-1-phosphate phosphatase 1. (PMID:35081855)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	sgpp1b	ENSDARG00000060534
danio_rerio	sgpp1a	ENSDARG00000079369
mus_musculus	Sgpp1	ENSMUSG00000021054
rattus_norvegicus	Sgpp1	ENSRNOG00000005175
drosophila_melanogaster	CG31717	FBGN0051717
caenorhabditis_elegans		WBGENE00020486

Paralogs (3): PLPP7 (ENSG00000160539), SGPP2 (ENSG00000163082), PLPP6 (ENSG00000205808)

Protein

Protein identifiers

Sphingosine-1-phosphate phosphatase 1 — Q9BX95 (reviewed: Q9BX95)

Alternative names: Sphingosine-1-phosphatase 1, Sphingosine-1-phosphate phosphohydrolase 1

All UniProt accessions (1): Q9BX95

UniProt curated annotations — full annotation on UniProt →

Function. Specifically dephosphorylates sphingosine 1-phosphate (S1P), dihydro-S1P, and phyto-S1P. Does not act on ceramide 1-phosphate, lysophosphatidic acid or phosphatidic acid. Sphingosine-1-phosphate phosphatase activity is needed for efficient recycling of sphingosine into the sphingolipid synthesis pathway. Regulates the intracellular levels of the bioactive sphingolipid metabolite S1P that regulates diverse biological processes acting both as an extracellular receptor ligand or as an intracellular second messenger. Involved in efficient ceramide synthesis from exogenous sphingoid bases. Converts S1P to sphingosine, which is readily metabolized to ceramide via ceramide synthase. In concert with sphingosine kinase 2 (SphK2), recycles sphingosine into ceramide through a phosphorylation/dephosphorylation cycle. Regulates endoplasmic-to-Golgi trafficking of ceramides, resulting in the regulation of ceramide levels in the endoplasmic reticulum, preferentially long-chain ceramide species, and influences the anterograde membrane transport of both ceramide and proteins from the endoplasmic reticulum to the Golgi apparatus. The modulation of intracellular ceramide levels in turn regulates apoptosis. Via S1P levels, modulates resting tone, intracellular Ca(2+) and myogenic vasoconstriction in resistance arteries. Also involved in unfolded protein response (UPR) and ER stress-induced autophagy via regulation of intracellular S1P levels. Involved in the regulation of epidermal homeostasis and keratinocyte differentiation.

Subcellular location. Endoplasmic reticulum membrane. Cell membrane.

Tissue specificity. Ubiquitous, with the strongest level in placenta and kidney.

Similarity. Belongs to the type 2 lipid phosphate phosphatase family.

RefSeq proteins (1): NP_110418* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000326	PAP2/HPO	Domain
IPR036938	PAP2/HPO_sf	Homologous_superfamily

Pfam: PF01569

Catalyzed reactions (Rhea), 2 shown:

• sphinganine 1-phosphate + H2O = sphinganine + phosphate (RHEA:27514)
• sphing-4-enine 1-phosphate + H2O = sphing-4-enine + phosphate (RHEA:27518)

UniProt features (29 total): transmembrane region 9, sequence conflict 7, region of interest 4, modified residue 3, active site 2, chain 1, compositionally biased region 1, site 1, mutagenesis site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BX95-F1	81.76	0.62

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (3): 208 (proton donor); 255 (nucleophile); 259 (stabilizes the active site histidine for nucleophilic attack)

Post-translational modifications (3): 101, 112, 114

Mutagenesis-validated functional residues (1):

Position	Phenotype
208	abolishes phosphatase activity.

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-9845614	Sphingolipid catabolism
R-HSA-1430728	Metabolism
R-HSA-428157	Sphingolipid metabolism
R-HSA-556833	Metabolism of lipids

MSigDB gene sets: 229 (showing top): GOBP_LIPID_MODIFICATION, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, WANG_CLIM2_TARGETS_UP, GOBP_REGULATION_OF_EPIDERMIS_DEVELOPMENT, GOBP_PHOSPHOLIPID_DEPHOSPHORYLATION, GOBP_POLYOL_METABOLIC_PROCESS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_EXTRINSIC_APOPTOTIC_SIGNALING_PATHWAY, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_SMAD4_DN, GOBP_MEMBRANE_LIPID_CATABOLIC_PROCESS, GOBP_REGULATION_OF_EPITHELIAL_CELL_DIFFERENTIATION, GTGCCTT_MIR506

GO Biological Process (11): sphinganine-1-phosphate metabolic process (GO:0006668), sphingosine metabolic process (GO:0006670), sphingolipid catabolic process (GO:0030149), ER to Golgi ceramide transport (GO:0035621), regulation of keratinocyte differentiation (GO:0045616), regulation of epidermis development (GO:0045682), phospholipid dephosphorylation (GO:0046839), extrinsic apoptotic signaling pathway (GO:0097191), intrinsic apoptotic signaling pathway (GO:0097193), lipid metabolic process (GO:0006629), sphingolipid metabolic process (GO:0006665)

GO Molecular Function (3): sphingosine-1-phosphate phosphatase activity (GO:0042392), dihydrosphingosine-1-phosphate phosphatase activity (GO:0070780), hydrolase activity (GO:0016787)

GO Cellular Component (4): endoplasmic reticulum membrane (GO:0005789), plasma membrane (GO:0005886), endoplasmic reticulum (GO:0005783), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Sphingolipid metabolism	1
Metabolism of lipids	1
Metabolism	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
sphingolipid metabolic process	2
apoptotic signaling pathway	2
phospholipid metabolic process	1
diol metabolic process	1
sphingoid metabolic process	1
lipid catabolic process	1
intracellular lipid transport	1
ceramide transport	1
keratinocyte differentiation	1
regulation of epidermal cell differentiation	1
epidermis development	1
regulation of developmental process	1
dephosphorylation	1
lipid modification	1
cell surface receptor signaling pathway	1
intracellular signal transduction	1
primary metabolic process	1
lipid metabolic process	1
lipid phosphatase activity	1
phosphatase activity	1
catalytic activity	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
membrane	1
cell periphery	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

752 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SGPP1	SPHK2	Q9NRA0	901
SGPP1	TLCD3B	Q71RH2	898
SGPP1	SGPL1	O95470	790
SGPP1	UBP1	Q9NZI7	760
SGPP1	SPHK1	Q9NYA1	735
SGPP1	S1PR3	Q99500	587
SGPP1	SPNS2	Q8IVW8	584
SGPP1	S1PR2	O95136	573
SGPP1	SPTLC1	O15269	571
SGPP1	SPTLC3	Q9NUV7	570
SGPP1	ASAH1	Q13510	552
SGPP1	CERS4	Q9HA82	552
SGPP1	CERK	Q8TCT0	537
SGPP1	SPTLC2	O15270	519
SGPP1	ACER3	Q9NUN7	501

IntAct

64 interactions, top by confidence:

A	B	Type	Score
SCGN	SNAP23	psi-mi:“MI:0914”(association)	0.550
SLC7A1	TMEM223	psi-mi:“MI:0914”(association)	0.530
ADGRG5	KLRG2	psi-mi:“MI:0914”(association)	0.530
MAS1	POTEF	psi-mi:“MI:0914”(association)	0.530
DLK1	TCAF2	psi-mi:“MI:0914”(association)	0.530
SLC15A1	METTL15	psi-mi:“MI:0914”(association)	0.530
LAMP3	METTL15	psi-mi:“MI:0914”(association)	0.530
GABRE	FZD6	psi-mi:“MI:0914”(association)	0.530
GDPD5	GOLIM4	psi-mi:“MI:0914”(association)	0.530
MCOLN3	UPK3BL1	psi-mi:“MI:0914”(association)	0.530
CHST10	B4GAT1	psi-mi:“MI:0914”(association)	0.530
TM2D2	TMEM97	psi-mi:“MI:0914”(association)	0.530
YIPF3	TMEM120B	psi-mi:“MI:0914”(association)	0.530
SLC22A9	GPR89A	psi-mi:“MI:0914”(association)	0.530
SYP	APBB1	psi-mi:“MI:0914”(association)	0.530
SLC22A16	APBA3	psi-mi:“MI:0914”(association)	0.530
RHOT2	UBC	psi-mi:“MI:0914”(association)	0.530
LPAR1	TMEM223	psi-mi:“MI:0914”(association)	0.530
TUBG1	DPM1	psi-mi:“MI:0914”(association)	0.350
TMEM63B	CAV1	psi-mi:“MI:0914”(association)	0.350
GOLT1B		psi-mi:“MI:0914”(association)	0.350
YIPF3	TMEM223	psi-mi:“MI:0914”(association)	0.350
ERGIC3	TMEM223	psi-mi:“MI:0914”(association)	0.350
ASIC4	UPK3BL1	psi-mi:“MI:0914”(association)	0.350

BioGRID (80): SGPP1 (Affinity Capture-MS), SGPP1 (Affinity Capture-MS), SGPP1 (Affinity Capture-MS), SGPP1 (Affinity Capture-MS), SGPP1 (Affinity Capture-MS), SGPP1 (Affinity Capture-MS), SGPP1 (Affinity Capture-MS), SGPP1 (Affinity Capture-MS), SGPP1 (Affinity Capture-MS), SGPP1 (Affinity Capture-MS), SGPP1 (Affinity Capture-MS), SGPP1 (Affinity Capture-MS), SGPP1 (Affinity Capture-MS), SGPP1 (Affinity Capture-MS), SGPP1 (Affinity Capture-MS)

ESM2 similar proteins: A0JNC1, A2VE61, A7XZ53, B1H3H9, D3ZEH5, F4HXY7, O35052, O95674, P48651, P98191, Q00576, Q01685, Q0JR55, Q0VCK9, Q28CY9, Q28H54, Q2KHY9, Q5EA65, Q5N8Q3, Q5R7B1, Q5U239, Q5ZKD1, Q5ZKJ0, Q5ZM65, Q6AXM5, Q6DD44, Q6DED0, Q6I628, Q7ZYQ3, Q803C9, Q8BGS7, Q8BXA5, Q8CIF6, Q8NBJ9, Q91XU8, Q91ZQ0, Q92903, Q96KA5, Q99KU0, Q99L43

Diamond homologs: P42334, P75806, P80143, Q1MA49, Q2K2U9, Q57819, Q810K3, Q8IWX5, Q99P55, Q9BX95, Q9JI99, Q55A00, P23501, P47013

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 78 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO term	Partners	Fold	FDR
adenylate cyclase-activating G protein-coupled receptor signaling pathway	6	10.4×	8e-03
G protein-coupled receptor signaling pathway	9	5.0×	8e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

68 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	61
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

697 predictions. Top by Δscore:

Variant	Effect	Δscore
14:63686655:TC:T	acceptor_gain	1.0000
14:63686656:CC:C	acceptor_gain	1.0000
14:63686656:CCTA:C	acceptor_loss	1.0000
14:63686657:C:CA	acceptor_loss	1.0000
14:63686658:T:C	acceptor_loss	1.0000
14:63698659:C:CC	acceptor_gain	1.0000
14:63702993:TATC:T	donor_gain	1.0000
14:63686652:ATATC:A	acceptor_gain	0.9900
14:63686653:TATC:T	acceptor_gain	0.9900
14:63686657:C:CC	acceptor_gain	0.9900
14:63698654:GGGTA:G	acceptor_gain	0.9900
14:63698657:TA:T	acceptor_gain	0.9900
14:63702168:TA:T	donor_gain	0.9900
14:63702169:AA:A	donor_gain	0.9900
14:63702169:AAC:A	donor_gain	0.9900
14:63702170:A:C	donor_gain	0.9900
14:63702989:C:CT	donor_gain	0.9900
14:63702990:T:TT	donor_gain	0.9900
14:63722891:AAG:A	donor_gain	0.9900
14:63727255:CCCTA:C	donor_loss	0.9900
14:63727256:CCTAC:C	donor_loss	0.9900
14:63727257:CTACC:C	donor_loss	0.9900
14:63727258:TAC:T	donor_loss	0.9900
14:63727259:A:T	donor_loss	0.9900
14:63727260:C:G	donor_loss	0.9900
14:63727263:G:A	donor_gain	0.9900
14:63727345:A:AC	donor_gain	0.9900
14:63686597:C:CT	acceptor_gain	0.9800
14:63686654:ATC:A	acceptor_gain	0.9800
14:63698655:GGTA:G	acceptor_gain	0.9800

AlphaMissense

2836 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
14:63698599:A:C	S248R	0.999
14:63698599:A:T	S248R	0.999
14:63698601:T:G	S248R	0.999
14:63727411:C:A	K178N	0.999
14:63727411:C:G	K178N	0.999
14:63686199:A:T	V411D	0.998
14:63686466:A:T	I322K	0.998
14:63686484:C:G	R316P	0.998
14:63686492:G:C	S313R	0.998
14:63686492:G:T	S313R	0.998
14:63686494:T:G	S313R	0.998
14:63698597:C:G	R249T	0.998
14:63698600:C:A	S248I	0.998
14:63727321:A:C	H208Q	0.998
14:63727321:A:T	H208Q	0.998
14:63727331:G:T	P205H	0.998
14:63727391:C:A	R185M	0.998
14:63727391:C:G	R185T	0.998
14:63727409:T:G	D179A	0.998
14:63727446:A:G	W167R	0.998
14:63727446:A:T	W167R	0.998
14:63686184:C:G	R416P	0.997
14:63686460:C:T	G324E	0.997
14:63686461:C:G	G324R	0.997
14:63686461:C:T	G324R	0.997
14:63686463:A:G	L323P	0.997
14:63686466:A:C	I322R	0.997
14:63686472:G:T	A320D	0.997
14:63686487:G:A	S315F	0.997
14:63686495:C:A	W312C	0.997

dbSNP variants (sampled 300 via entrez): RS1000218581 (14:63717641 G>A), RS1000345584 (14:63689570 G>A,T), RS1000351708 (14:63711576 T>A,C), RS1000368969 (14:63717596 A>G), RS1000422426 (14:63724076 C>T), RS1000457602 (14:63705870 A>G), RS1000542715 (14:63695142 C>T), RS1000655796 (14:63717894 C>T), RS1000664693 (14:63699890 C>G,T), RS1000721729 (14:63711424 A>C), RS1000775765 (14:63711679 T>C), RS1000814051 (14:63687904 T>C), RS1000866569 (14:63688076 G>T), RS1000970250 (14:63688221 C>G), RS1000993465 (14:63699730 T>C,G)

Disease associations

OMIM: gene MIM:612826 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

51 associations (top):

Study	Trait	p-value
GCST000493_3	Sphingolipid levels	9.000000e-66
GCST001413_2	Sphingolipid levels	3.000000e-57
GCST005648_25	Serum metabolite concentrations in chronic kidney disease	7.000000e-15
GCST005648_26	Serum metabolite concentrations in chronic kidney disease	5.000000e-12
GCST005650_209	Serum metabolite ratios in chronic kidney disease	5.000000e-22
GCST008933_22	Sphingomyelin levels	5.000000e-06
GCST009152_8	Triglyceride levels	5.000000e-15
GCST009391_745	Metabolite levels	3.000000e-10
GCST009391_747	Metabolite levels	3.000000e-07
GCST009698_10	Metabolite levels	2.000000e-12
GCST009698_11	Metabolite levels	2.000000e-09
GCST009698_112	Metabolite levels	8.000000e-11
GCST009698_114	Metabolite levels	1.000000e-16
GCST009698_121	Metabolite levels	9.000000e-10
GCST009698_123	Metabolite levels	2.000000e-09
GCST009698_125	Metabolite levels	1.000000e-11
GCST009698_128	Metabolite levels	6.000000e-09
GCST009698_14	Metabolite levels	5.000000e-12
GCST009698_15	Metabolite levels	1.000000e-08
GCST009698_18	Metabolite levels	8.000000e-09
GCST009698_19	Metabolite levels	7.000000e-09
GCST009698_20	Metabolite levels	2.000000e-08
GCST009698_35	Metabolite levels	1.000000e-08
GCST009698_4	Metabolite levels	1.000000e-15
GCST009698_45	Metabolite levels	4.000000e-13
GCST009698_46	Metabolite levels	1.000000e-09
GCST009698_5	Metabolite levels	8.000000e-12
GCST009698_50	Metabolite levels	2.000000e-10
GCST009698_51	Metabolite levels	3.000000e-09
GCST009698_6	Metabolite levels	2.000000e-23

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0010118	sphingomyelin measurement
EFO:0004530	triglyceride measurement
EFO:0010390	sphingomyelin 14:0 measurement
EFO:0004611	low density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — Sphingosine 1-phosphate phosphatase

CTD chemical–gene interactions

34 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression	6
trichostatin A	affects cotreatment, increases expression	3
methylmercuric chloride	decreases expression	2
sodium arsenite	decreases expression, increases expression	2
Panobinostat	affects cotreatment, increases expression	2
Cadmium	increases expression, increases abundance	2
FR900359	decreases phosphorylation	1
daidzein	affects cotreatment, decreases expression	1
triphenyl phosphate	affects expression	1
di-n-butylphosphoric acid	affects expression	1
glycitein	affects cotreatment, decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
picoxystrobin	increases expression	1
(+)-JQ1 compound	increases expression	1
Bortezomib	increases expression	1
Sunitinib	increases expression	1
Air Pollutants	increases abundance, decreases expression	1
Bilirubin	decreases expression	1
Caffeine	increases phosphorylation	1
Cisplatin	decreases expression	1
Diethylhexyl Phthalate	increases expression	1
Dimethyl Sulfoxide	increases expression	1
Doxorubicin	decreases expression	1
Phthalic Acids	increases methylation	1
Tetrachlorodibenzodioxin	affects expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Urethane	increases expression	1
Aflatoxin B1	increases methylation	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.