SPNS1

Summary

SPNS1 (SPNS lysolipid transporter 1, lysophospholipid, HGNC:30621) is a protein-coding gene on chromosome 16p11.2, encoding Protein spinster homolog 1 (Q9H2V7). Plays a critical role in the phospholipid salvage pathway from lysosomes to the cytosol.

Predicted to enable transmembrane transporter activity. Predicted to be involved in lysophospholipid transport and phospholipid efflux. Predicted to act upstream of or within regulation of lysosomal lumen pH. Located in lysosomal membrane.

Source: NCBI Gene 83985 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 81 total — 1 pathogenic, 1 likely-pathogenic
• Phenotypes (HPO): 27
• MANE Select transcript: NM_032038

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30621
Approved symbol	SPNS1
Name	SPNS lysolipid transporter 1, lysophospholipid
Location	16p11.2
Locus type	gene with protein product
Status	Approved
Aliases	HSpin1, nrs, SPINL, PP2030, SPIN1, LAT, SLC63A1
Ensembl gene	ENSG00000169682
Ensembl biotype	protein_coding
OMIM	612583
Entrez	83985

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 10 protein_coding, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000311008, ENST00000323081, ENST00000334536, ENST00000352260, ENST00000561868, ENST00000564476, ENST00000565975, ENST00000566059, ENST00000567771, ENST00000568388, ENST00000568829, ENST00000568900

RefSeq mRNA: 5 — MANE Select: NM_032038 NM_001142448, NM_001142449, NM_001142450, NM_001142451, NM_032038

CCDS: CCDS10646, CCDS45452, CCDS45453, CCDS45454

Canonical transcript exons

ENST00000311008 — 12 exons

Exon	Start	End
ENSE00001168403	28982356	28982545
ENSE00001168412	28981901	28982056
ENSE00001614308	28974778	28975392
ENSE00002611822	28984205	28984543
ENSE00003496337	28982857	28982922
ENSE00003524949	28977908	28978044
ENSE00003563612	28983192	28983290
ENSE00003566821	28979155	28979306
ENSE00003623033	28975492	28975557
ENSE00003666446	28981470	28981615
ENSE00003687245	28979405	28979471
ENSE00003694468	28983786	28983957

Expression profiles

Bgee: expression breadth ubiquitous, 144 present calls, max score 94.44.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 56.2657 / max 229.6371, expressed in 1819 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
153440	55.4217	1819
153441	0.6946	340
153439	0.1494	37

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	94.44	gold quality
stromal cell of endometrium	CL:0002255	93.37	gold quality
monocyte	CL:0000576	92.13	gold quality
leukocyte	CL:0000738	92.11	gold quality
popliteal artery	UBERON:0002250	91.80	gold quality
tibial artery	UBERON:0007610	91.79	gold quality
spleen	UBERON:0002106	91.68	gold quality
mucosa of transverse colon	UBERON:0004991	91.58	gold quality
metanephros cortex	UBERON:0010533	91.55	gold quality
skin of leg	UBERON:0001511	91.39	gold quality
descending thoracic aorta	UBERON:0002345	91.20	gold quality
muscle layer of sigmoid colon	UBERON:0035805	91.10	gold quality
mucosa of stomach	UBERON:0001199	91.09	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	91.09	gold quality
cortex of kidney	UBERON:0001225	91.01	gold quality
right adrenal gland cortex	UBERON:0035827	91.00	gold quality
right coronary artery	UBERON:0001625	90.95	gold quality
upper lobe of left lung	UBERON:0008952	90.94	gold quality
zone of skin	UBERON:0000014	90.90	gold quality
left coronary artery	UBERON:0001626	90.80	gold quality
right adrenal gland	UBERON:0001233	90.77	gold quality
body of uterus	UBERON:0009853	90.63	gold quality
left adrenal gland	UBERON:0001234	90.61	gold quality
lower esophagus muscularis layer	UBERON:0035833	90.60	gold quality
body of stomach	UBERON:0001161	90.59	gold quality
lower esophagus	UBERON:0013473	90.59	gold quality
left adrenal gland cortex	UBERON:0035825	90.59	gold quality
skin of abdomen	UBERON:0001416	90.55	gold quality
small intestine Peyer’s patch	UBERON:0003454	90.39	gold quality
fundus of stomach	UBERON:0001160	90.35	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-MTAB-6386	no	69.66
E-ANND-3	no	2.62

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): YY1

miRNA regulators (miRDB)

14 targeting SPNS1, 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-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-142-3P	99.62	71.30	974
HSA-MIR-4651	99.06	67.57	2002
HSA-MIR-608	98.93	67.83	2013
HSA-MIR-4726-3P	98.49	63.89	1385
HSA-MIR-4640-5P	97.42	66.33	1543
HSA-MIR-3192-5P	96.98	65.76	1926
HSA-MIR-4794	96.47	65.53	1063
HSA-MIR-4300	95.85	64.56	1003
HSA-MIR-5591-5P	95.85	64.76	1002
HSA-MIR-664A-5P	95.84	64.93	949

Literature-anchored findings (GeneRIF, showing 5)

• Spinster protein interferes with programmed cell death in Drosophila melanogaster and has orthologs in nematode, mouse, and human. (PMID:11340170)
• A single nucleotide polymorphism located within the spns1 gene is associated with plasma triglyceride levels. (PMID:22942098)
• SPNS1-dependent L-leucine export across the lysosomal membrane is a key step for triggering autophagy, and that this mechanism is impaired in Niemann-Pick type C disease-1. (PMID:29162837)
• Spindlin 1 (SPIN1) sequesters ribosomal protein uL18 in the nucleolus, preventing it from interacting with c-mdm2 Proto-oncogene protein (MDM2), and alleviating uL18-mediated inhibition of MDM2 ubiquitin ligase activity toward p53 tumor suppressor protein (p53). (PMID:29547122)
• Spns1 is a lysosomal proton-dependent lysophosphatidylcholine (LPC) and lysophosphatidylethanolamine (LPE) transporter mediating phospholipid salvage pathway (PMID:36161949)

Cross-species orthologs

8 orthologs

Organism	Symbol	Gene ID
danio_rerio	spns1	ENSDARG00000011925
mus_musculus	Spns1	ENSMUSG00000030741
rattus_norvegicus	Spns1	ENSRNOG00000017621
drosophila_melanogaster	spin	FBGN0086676
caenorhabditis_elegans		WBGENE00007549
caenorhabditis_elegans		WBGENE00008033
caenorhabditis_elegans		WBGENE00008598
caenorhabditis_elegans		WBGENE00013739

Paralogs (2): SPNS3 (ENSG00000182557), SPNS2 (ENSG00000183018)

Protein

Protein identifiers

Protein spinster homolog 1 — Q9H2V7 (reviewed: Q9H2V7)

Alternative names: HSpin1, SPNS1, Spinster-like protein 1

All UniProt accessions (7): Q9H2V7, H3BMF4, H3BP14, H3BPQ9, H3BPT8, H3BR82, H3BT44

UniProt curated annotations — full annotation on UniProt →

Function. Plays a critical role in the phospholipid salvage pathway from lysosomes to the cytosol. Mediates the rate-limiting, proton-dependent, lysosomal efflux of lysophospholipids, which can then be reacylated by acyltransferases in the endoplasmic reticulum to form phospholipids. Selective for zwitterionic headgroups such as lysophosphatidylcholine (LPC) and lysophosphatidylethanolamine (LPE), can also transport lysophosphatidylglycerol (LPG), but not other anionic lysophospholipids, sphingosine, nor sphingomyelin. Transports lysophospholipids with saturated, monounsaturated, and polyunsaturated fatty acids, such as 1-hexadecanoyl-sn-glycero-3-phosphocholine, 1-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine and 1-(4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl)-sn-glycero-3-phosphocholine, respectively. Can also transport lysoplasmalogen (LPC with a fatty alcohol) such as 1-(1Z-hexadecenyl)-sn-glycero-3-phosphocholine. Lysosomal LPC could function as intracellular signaling messenger. Essential player in lysosomal homeostasis. Crucial for cell survival under conditions of nutrient limitation. May be involved in necrotic or autophagic cell death.

Subunit / interactions. Interacts with BCL2 and BCL2L1.

Subcellular location. Lysosome membrane. Mitochondrion inner membrane.

Similarity. Belongs to the major facilitator superfamily. Spinster (TC 2.A.1.49) family.

Isoforms (5)

UniProt ID	Names	Canonical?
Q9H2V7-1	1	yes
Q9H2V7-2	2
Q9H2V7-3	3, CRA_d
Q9H2V7-4	4
Q9H2V7-5	5

RefSeq proteins (5): NP_001135920, NP_001135921, NP_001135922, NP_001135923, NP_114427* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011701	MFS	Family
IPR020846	MFS_dom	Domain
IPR036259	MFS_trans_sf	Homologous_superfamily
IPR044770	MFS_spinster-like	Family

Pfam: PF07690

Catalyzed reactions (Rhea), 12 shown:

• 1-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine(out) + H(+)(out) = 1-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine(in) + H(+)(in) (RHEA:74411)
• 1-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine(out) + H(+)(out) = 1-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine(in) + H(+)(in) (RHEA:74415)
• 1-(9Z-octadecenoyl)-sn-glycero-3-phospho-(1’-sn-glycerol)(out) + H(+)(out) = 1-(9Z-octadecenoyl)-sn-glycero-3-phospho-(1’-sn-glycerol)(in) + H(+)(in) (RHEA:74419)
• 1-(4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl)-sn-glycero-3-phosphocholine(out) + H(+)(out) = 1-(4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl)-sn-glycero-3-phosphocholine(in) + H(+)(in) (RHEA:74423)
• 1-hexadecanoyl-sn-glycero-3-phosphocholine(out) + H(+)(out) = 1-hexadecanoyl-sn-glycero-3-phosphocholine(in) + H(+)(in) (RHEA:74427)
• 1-(1Z-hexadecenyl)-sn-glycero-3-phosphocholine(out) + H(+)(out) = 1-(1Z-hexadecenyl)-sn-glycero-3-phosphocholine(in) + H(+)(in) (RHEA:74431)
• a 1-acyl-sn-glycero-3-phosphocholine(out) + H(+)(out) = a 1-acyl-sn-glycero-3-phosphocholine(in) + H(+)(in) (RHEA:74435)
• a 1-acyl-sn-glycero-3-phosphoethanolamine(out) + H(+)(out) = a 1-acyl-sn-glycero-3-phosphoethanolamine(in) + H(+)(in) (RHEA:74439)
• 1-acyl-sn-glycero-3-phospho-(1’-sn-glycerol)(out) + H(+)(out) = 1-acyl-sn-glycero-3-phospho-(1’-sn-glycerol)(in) + H(+)(in) (RHEA:74443)
• a 1-O-(1Z-alkenyl)-sn-glycero-3-phosphocholine(out) + H(+)(out) = a 1-O-(1Z-alkenyl)-sn-glycero-3-phosphocholine(in) + H(+)(in) (RHEA:74447)
• 1-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phosphocholine(out) + H(+)(out) = 1-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phosphocholine(in) + H(+)(in) (RHEA:74451)
• a 1-O-(1Z-alkenyl)-sn-glycero-3-phosphoethanolamine(out) + H(+)(out) = a 1-O-(1Z-alkenyl)-sn-glycero-3-phosphoethanolamine(in) + H(+)(in) (RHEA:74455)

UniProt features (43 total): helix 18, transmembrane region 12, splice variant 4, modified residue 2, turn 2, initiator methionine 1, chain 1, region of interest 1, sequence variant 1, strand 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
9BOI	ELECTRON MICROSCOPY	3.22

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H2V7-F1	84.82	0.67

Functional residue map

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

Post-translational modifications (2): 2, 518

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 715 (showing top): GOBP_REGULATION_OF_CELL_ACTIVATION, RNGTGGGC_UNKNOWN, REACTOME_INNATE_IMMUNE_SYSTEM, GOBP_VACUOLE_ORGANIZATION, GOBP_REGULATION_OF_PHOSPHORYLATION, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, MODULE_255, GOBP_INFLAMMATORY_RESPONSE, GOCC_VACUOLAR_MEMBRANE, REACTOME_PLATELET_ACTIVATION_SIGNALING_AND_AGGREGATION, TTTGTAG_MIR520D, MODULE_64, GOBP_LYMPHOCYTE_HOMEOSTASIS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GOBP_ANTIGEN_RECEPTOR_MEDIATED_SIGNALING_PATHWAY

GO Biological Process (5): phospholipid efflux (GO:0033700), obsolete regulation of lysosomal lumen pH (GO:0035751), lysophospholipid transport (GO:0051977), lipid transport (GO:0006869), transmembrane transport (GO:0055085)

GO Molecular Function (3): transmembrane transporter activity (GO:0022857), lysophospholipid:sodium symporter activity (GO:0051978), protein binding (GO:0005515)

GO Cellular Component (6): mitochondrial inner membrane (GO:0005743), lysosome (GO:0005764), lysosomal membrane (GO:0005765), membrane (GO:0016020), mitochondrion (GO:0005739), endomembrane system (GO:0012505)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
phospholipid transport	2
transport	2
cellular anatomical structure	2
carbohydrate derivative transport	1
lipid localization	1
cellular process	1
transporter activity	1
transmembrane transport	1
solute:sodium symporter activity	1
organophosphate ester transmembrane transporter activity	1
lysophospholipid transport	1
lipid transmembrane transporter activity	1
carbohydrate derivative transmembrane transporter activity	1
binding	1
organelle inner membrane	1
mitochondrial membrane	1
lytic vacuole	1
lysosome	1
lytic vacuole membrane	1
cytoplasm	1
intracellular membrane-bounded organelle	1
vacuole	1
plasma membrane	1

Protein interactions and networks

STRING

1106 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPNS1	MFSD2B	A6NFX1	857
SPNS1	BCL2L1	Q07817	658
SPNS1	SLC67A2	Q8NBP5	643
SPNS1	BCL2	P10415	613
SPNS1	CTSD	P07339	609
SPNS1	SLC75A1	Q14728	572
SPNS1	RABEP2	Q9H5N1	570
SPNS1	SVOP	Q8N4V2	564
SPNS1	MFSD11	O43934	539
SPNS1	TUFM	P49411	530
SPNS1	PIN1	Q13526	518
SPNS1	ATXN2L	Q8WWM7	507
SPNS1	SH2B1	Q9NRF2	478
SPNS1	UNC93A	Q86WB7	476
SPNS1	NFATC2IP	Q8NCF5	475

IntAct

74 interactions, top by confidence:

A	B	Type	Score
CA10	WDHD1	psi-mi:“MI:0914”(association)	0.640
AUP1	APOB	psi-mi:“MI:0914”(association)	0.610
TNFSF8	LGALS8	psi-mi:“MI:0914”(association)	0.530
ARMC6	SLC27A2	psi-mi:“MI:0914”(association)	0.530
SLC6A8	ILVBL	psi-mi:“MI:0914”(association)	0.530
SPNS1	BCL2	psi-mi:“MI:0915”(physical association)	0.460
SPNS1	BCL2L1	psi-mi:“MI:0915”(physical association)	0.460
BCL2	SPNS1	psi-mi:“MI:0403”(colocalization)	0.460
BCL2L1	SPNS1	psi-mi:“MI:0403”(colocalization)	0.460
FLT4	ILVBL	psi-mi:“MI:0914”(association)	0.420
SPNS1	HTR2C	psi-mi:“MI:0915”(physical association)	0.370
SPNS1	ADORA2A	psi-mi:“MI:0915”(physical association)	0.370
SPNS1	BDKRB2	psi-mi:“MI:0915”(physical association)	0.370
SPNS1	CCR8	psi-mi:“MI:0915”(physical association)	0.370
SPNS1	CCR9	psi-mi:“MI:0915”(physical association)	0.370
SPNS1	CHRM5	psi-mi:“MI:0915”(physical association)	0.370
		psi-mi:“MI:0914”(association)	0.350
	ESYT2	psi-mi:“MI:0914”(association)	0.350
E5	ESYT2	psi-mi:“MI:0914”(association)	0.350
	PGRMC1	psi-mi:“MI:0914”(association)	0.350
	HAX1	psi-mi:“MI:0914”(association)	0.350
HSCB	RBP5	psi-mi:“MI:0914”(association)	0.350
	TSPO	psi-mi:“MI:0914”(association)	0.350
USP19		psi-mi:“MI:0914”(association)	0.350
	TMEM223	psi-mi:“MI:0914”(association)	0.350

BioGRID (113): SPNS1 (Affinity Capture-MS), SPNS1 (Affinity Capture-MS), SPNS1 (Affinity Capture-MS), SPNS1 (Affinity Capture-MS), BCL2 (Affinity Capture-Western), BCL2L1 (Affinity Capture-Western), SPNS1 (Affinity Capture-MS), SPNS1 (Affinity Capture-MS), SPNS1 (Co-fractionation), NPTN (Co-fractionation), SPNS1 (Affinity Capture-MS), SPNS1 (Affinity Capture-MS), SPNS1 (Affinity Capture-MS), SPNS1 (Affinity Capture-MS), SPNS1 (Affinity Capture-MS)

ESM2 similar proteins: A0A3Q2HW92, A6NDV4, A6NFX1, A6QLK4, B1AWJ5, F1NCD6, F1NJ67, F1PZV2, O35308, O35595, O70461, O95907, Q08DX7, Q0IHM1, Q0P5C0, Q0P5M9, Q13286, Q14728, Q29611, Q2YDU8, Q3T9M1, Q3U481, Q501I9, Q5R8G5, Q5R9A1, Q5U419, Q60HH0, Q61124, Q66H95, Q6NUT3, Q6UXD7, Q6ZMD2, Q7RTT9, Q8BFQ6, Q8CE47, Q8NA29, Q8R0G7, Q8R139, Q8TB61, Q8VCW4

Diamond homologs: A2CER7, A2SWM2, A8WGF7, B0JZE1, P96712, Q08DX7, Q2YDU8, Q5XGK0, Q6ZMD2, Q7ZU13, Q8IVW8, Q8R0G7, Q91VM4, Q9D232, Q9GQQ0, Q9H2V7, O31762, Q796Q1, S0DW25, A4FV52, A6QLI1, O00624, O61369, O82390, O95528, P0AA78, P0AA79, P40760, P77589, P9WJW6, P9WJW7, Q03567, Q05B21, Q0IZQ3, Q1L8X9, Q3E9A0, Q3TXX4, Q53WP9, Q5ATG7, Q5Q0U0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	1
Uncertain significance	54
Likely benign	6
Benign	1

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
2685565	GRCh37/hg19 16p11.2(chr16:28819029-29088624)x1	Pathogenic
929355	GRCh37/hg19 16p11.2(chr16:28825605-29043450)x3	Likely pathogenic

SpliceAI

1718 predictions. Top by Δscore:

Variant	Effect	Δscore
16:28975388:GGCTG:G	donor_gain	1.0000
16:28975389:GCTGG:G	donor_gain	1.0000
16:28975391:TGGT:T	donor_loss	1.0000
16:28975392:GGTA:G	donor_loss	1.0000
16:28975393:G:GA	donor_loss	1.0000
16:28975393:G:GG	donor_gain	1.0000
16:28975394:T:A	donor_loss	1.0000
16:28975553:GACCG:G	donor_gain	1.0000
16:28977906:A:AG	acceptor_gain	1.0000
16:28977907:G:GG	acceptor_gain	1.0000
16:28977907:GT:G	acceptor_gain	1.0000
16:28977972:G:GT	donor_gain	1.0000
16:28978041:AGAGG:A	donor_loss	1.0000
16:28978043:AGGT:A	donor_loss	1.0000
16:28978045:G:GC	donor_loss	1.0000
16:28978046:T:G	donor_loss	1.0000
16:28979304:CAG:C	donor_loss	1.0000
16:28979305:AGGTG:A	donor_loss	1.0000
16:28979401:ACAGT:A	acceptor_gain	1.0000
16:28979403:A:AG	acceptor_gain	1.0000
16:28979403:AGT:A	acceptor_gain	1.0000
16:28979404:G:GA	acceptor_gain	1.0000
16:28979404:GTG:G	acceptor_gain	1.0000
16:28979404:GTGGT:G	acceptor_gain	1.0000
16:28979470:GG:G	donor_gain	1.0000
16:28979471:GG:G	donor_gain	1.0000
16:28981612:GAAA:G	donor_gain	1.0000
16:28981616:G:GG	donor_gain	1.0000
16:28982354:A:AG	acceptor_gain	1.0000
16:28982355:G:GA	acceptor_gain	1.0000

AlphaMissense

3360 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:28975358:T:A	N69K	1.000
16:28975358:T:G	N69K	1.000
16:28975367:C:A	N72K	1.000
16:28975367:C:G	N72K	1.000
16:28975374:G:C	D75H	1.000
16:28975377:C:A	R76S	1.000
16:28975378:G:C	R76P	1.000
16:28977910:T:C	F104L	1.000
16:28977912:C:A	F104L	1.000
16:28977912:C:G	F104L	1.000
16:28977947:G:A	G116D	1.000
16:28979191:G:A	G161R	1.000
16:28979191:G:C	G161R	1.000
16:28979191:G:T	G161W	1.000
16:28979192:G:A	G161E	1.000
16:28979198:G:A	G163E	1.000
16:28979206:A:C	S166R	1.000
16:28979208:T:A	S166R	1.000
16:28979208:T:G	S166R	1.000
16:28979234:T:A	I175N	1.000
16:28979302:G:C	G198R	1.000
16:28979303:G:A	G198D	1.000
16:28979412:G:C	G202R	1.000
16:28979413:G:A	G202D	1.000
16:28979413:G:T	G202V	1.000
16:28979454:T:A	W216R	1.000
16:28979454:T:C	W216R	1.000
16:28979456:G:C	W216C	1.000
16:28979456:G:T	W216C	1.000
16:28982367:G:A	G326E	1.000

dbSNP variants (sampled 300 via entrez): RS1000370819 (16:28980318 A>G,T), RS1000392918 (16:28974166 C>T), RS1000443518 (16:28974002 T>C), RS1000480150 (16:28974580 A>C,T), RS1001129876 (16:28985089 G>A,T), RS1001182497 (16:28974636 T>A,C), RS1001881250 (16:28979958 G>T), RS1001941186 (16:28973844 A>G), RS1001990512 (16:28973661 T>C), RS1002201265 (16:28973082 G>A), RS1002230302 (16:28979631 G>A), RS1002317454 (16:28973395 G>T), RS1002480063 (16:28979956 G>A,T), RS1002679816 (16:28984504 G>A), RS1002817260 (16:28977917 C>G,T)

Disease associations

OMIM: gene MIM:612583 | disease phenotypes:

GenCC curated gene-disease

Mondo (2): attention deficit-hyperactivity disorder (MONDO:0007743), hyperbilirubinemia (MONDO:0024288)

Orphanet (0):

HPO phenotypes

27 total (27 of 27 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0001508	Failure to thrive
HP:0001522	Death in infancy
HP:0001744	Splenomegaly
HP:0001888	Decreased total lymphocyte count
HP:0001973	Autoimmune thrombocytopenia
HP:0002110	Bronchiectasis
HP:0002716	Lymphadenopathy
HP:0002719	Recurrent infections
HP:0002720	Decreased circulating IgA concentration
HP:0002721	Immunodeficiency
HP:0002958	Immune dysregulation
HP:0003593	Infantile onset
HP:0003623	Neonatal onset
HP:0003819	Death in childhood
HP:0004313	Decreased circulating immunoglobulin concentration
HP:0004844	Coombs-positive hemolytic anemia
HP:0005403	Decreased total T cell count
HP:0006528	Chronic lung disease
HP:0006532	Recurrent pneumonia
HP:0010975	Abnormal B cell count
HP:0020072	Persistent EBV viremia
HP:0031379	Abnormal T cell proliferation
HP:0032218	Decreased CD4+ T cell proportion
HP:0032247	Persistent CMV viremia
HP:0040089	Abnormal total natural killer cell count
HP:0500270	Increased gamma-delta T cell proportion

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST002598_62	Educational attainment	1.000000e-06
GCST007732_19	Allergic disease (asthma, hay fever or eczema)	6.000000e-06
GCST007732_6	Allergic disease (asthma, hay fever or eczema)	5.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004784	self reported educational attainment

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D006932	Hyperbilirubinemia	C23.550.429

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: transporter — SLC63 Sphingosine phosphate transporters

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression, increases methylation	3
bisphenol A	increases expression, affects cotreatment, decreases expression	2
Benzo(a)pyrene	affects methylation, increases methylation	2
FR900359	decreases phosphorylation	1
bisphenol F	affects cotreatment, decreases expression	1
2,4,5,2’,4’,5’-hexachlorobiphenyl	increases expression	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
coumarin	increases phosphorylation	1
perfluorooctane sulfonic acid	increases expression	1
MT19c compound	decreases expression	1
Temozolomide	decreases expression	1
Sunitinib	increases expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Carbamazepine	affects expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Formaldehyde	increases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Ivermectin	decreases expression	1
Manganese	increases expression, affects cotreatment, increases abundance	1
Methyl Methanesulfonate	increases expression	1
Quercetin	decreases phosphorylation	1
Smoke	decreases expression	1
1-Methyl-3-isobutylxanthine	decreases expression, affects cotreatment	1
Aflatoxin B1	increases methylation	1

Cellosaurus cell lines

8 cell lines: 8 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_D4R4	HCT116-SPNS1-KO-c15	Cancer cell line	Male
CVCL_D4R5	HCT116-SPNS1-KO-c16	Cancer cell line	Male
CVCL_E0PV	Ubigene HeLa SPNS1 KO	Cancer cell line	Female
CVCL_TQ21	HAP1 SPNS1 (-) 1	Cancer cell line	Male
CVCL_XT74	HAP1 SPNS1 (-) 2	Cancer cell line	Male
CVCL_XT75	HAP1 SPNS1 (-) 3	Cancer cell line	Male
CVCL_XT76	HAP1 SPNS1 (-) 4	Cancer cell line	Male
CVCL_XT77	HAP1 SPNS1 (-) 5	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00152750	PHASE4	UNKNOWN	Study of Clonidine on Sleep Architecture in Children With Tourette’s Syndrome (TS) and Comorbid ADHD
NCT00181571	PHASE4	COMPLETED	A Double-Blind Comparison of Concerta and Placebo in Adults With Attention Deficit Hyperactivity Disorder
NCT00181675	PHASE4	COMPLETED	A Double-Blind Comparison of Galantamine HBr and Placebo in Adults With Attention Deficit Hyperactivity Disorder
NCT00181714	PHASE4	COMPLETED	Prevention of Cigarette Smoking in Attention Deficit Hyperactivity Disorder (ADHD) Youth With Concerta
NCT00181948	PHASE4	COMPLETED	Strattera Treatment in Children With ADHD Who Have Poor Response to Stimulant Therapy
NCT00181987	PHASE4	COMPLETED	Concerta in the Treatment of ADHD in Youth and Adults With Bipolar Disorder
NCT00190736	PHASE4	COMPLETED	Efficacy and Safety of Once-Daily Atomoxetine Hydrochloride in Adults With ADHD Over an Extended Period of Time (6 Months)
NCT00190775	PHASE4	COMPLETED	A Randomized, Double-Blind Comparison of Placebo and Atomoxetine Hydrochloride Given Once a Day in Adults With Attention-Deficit/Hyperactivity Disorder (ADHD)
NCT00190879	PHASE4	COMPLETED	Placebo-Controlled Study of Atomoxetine Hydrochloride in the Treatment of Adults With ADHD and Comorbid Social Anxiety Disorder
NCT00190957	PHASE4	COMPLETED	Atomoxetine Treatment of Adults With ADHD and Comorbid Alcohol Abuse
NCT00191035	PHASE4	COMPLETED	Maintenance of Benefit With Atomoxetine Hydrochloride in Adolescents With ADHD
NCT00191048	PHASE4	COMPLETED	Treatment With Atomoxetine Hydrochloride in Children and Adolescents With ADHD
NCT00191633	PHASE4	COMPLETED	Study of Atomoxetine in Children With ADHD to Assess Symptomatic and Functional Outcomes
NCT00191906	PHASE4	COMPLETED	Comparison of Atomoxetine and Placebo in Children With Attention-Deficit/Hyperactivity Disorder (ADHD) and/or Reading Disorder (RD)
NCT00216918	PHASE4	COMPLETED	Neuropsychological Functioning in Children With Attention-Deficit/Hyperactivity Disorder.
NCT00221962	PHASE4	COMPLETED	Study of Aripiprazole (Abilify) in Children With ADHD (Attention Deficit Hyperactivity Disorder)
NCT00223561	PHASE4	COMPLETED	Methylphenidate and Driving Ability in Adult Patients With Attention-Deficit Hyperactivity Disorder
NCT00299234	PHASE4	TERMINATED	Atomoxetine for Children With Acquired Attentional Disorders Following Completion of Chemotherapy for ALL
NCT00302406	PHASE4	COMPLETED	Naturalistic Substitution of Concerta in Adult Subject With ADHD Receiving Immediate Release Methylphenidate
NCT00305370	PHASE4	COMPLETED	Aripiprazole Associated With Methylphenidate in Children and Adolescents With Bipolar Disorder and ADHD
NCT00381758	PHASE4	COMPLETED	The COMACS Study: A Comparison of Methylphenidates in an Analog Classroom Setting
NCT00406354	PHASE4	COMPLETED	Comparison of Atomoxetine Versus Placebo in Children and Adolescents With ADHD and Comorbid ODD in Germany
NCT00434213	PHASE4	COMPLETED	Characterization of Dermal Reactions in Pediatric Patients With ADHD Using DAYTRANA
NCT00468143	PHASE4	COMPLETED	A Within-Subject Cross-Over Comparison Between Immediate Release and Extended Release Adderall
NCT00471354	PHASE4	COMPLETED	A Study for Patients With Attention-Deficit/Hyperactivity Disorder Treated With Atomoxetine
NCT00483106	PHASE4	COMPLETED	Clinical and Pharmacogenetic Study of Attention Deficit With Hyperactivity Disorder (ADHD)
NCT00485849	PHASE4	COMPLETED	A Study of Atomoxetine for Attention Deficit and Hyperactive/Impulsive Behaviour Problems in Children With ASD
NCT00485875	PHASE4	COMPLETED	Safety and Efficacy of Switching From a Stimulant Medication to Atomoxetine in Children and Adolescents With ADHD
NCT00486122	PHASE4	COMPLETED	Evaluation of Continuous Symptom Treatment of ADHD
NCT00500071	PHASE4	COMPLETED	Dose-Optimization Study Evaluating the Efficacy, Safety and Tolerability of Vyvanse (Lisdexamfetamine Dimesylate) in Children Aged 6-12 Diagnosed With ADHD
NCT00506727	PHASE4	COMPLETED	Analog Classroom Study Comparison of ADDERALL XR With STRATTERA in Children Aged 6-12 With ADHD
NCT00510276	PHASE4	COMPLETED	Treatment of Attention-Deficit/Hyperactivity Disorder (ADHD) With Atomoxetine in Young Adults and Its Effects on Functional Outcomes
NCT00517504	PHASE4	COMPLETED	Methylphenidate Study in Young Children With Developmental Disorders
NCT00517647	PHASE4	COMPLETED	Atomoxetine Pilot Study in Preschool Children With ADHD
NCT00518232	PHASE4	COMPLETED	A Study to Determine Effective and Tolerable Titration Scheme for OROS-Methylphenidate in Children With Attention-deficit Hyperactivity Disorder
NCT00530257	PHASE4	COMPLETED	Study of the Effects of Osmotic-Release Oral System (OROS) Methylphenidate (Concerta) on Attention and Memory
NCT00536419	PHASE4	UNKNOWN	Impact of Attention Deficit/Hyperactivity Disorder and Substance Use Disorder on Motorcycle Traffic Accidents
NCT00546910	PHASE4	COMPLETED	Comparison of Atomoxetine Versus Placebo in Children With Attention-Deficit/Hyperactivity Disorder (ADHD)
NCT00552266	PHASE4	UNKNOWN	Methylphenidate in ADHD With Trichotillomania
NCT00564954	PHASE4	COMPLETED	A Study of Dex-methylphenidate Extended Release in Children (6-12 Years) With Attention-Deficit/Hyperactivity Disorder (ADHD)