NPTN

Summary

NPTN (neuroplastin, HGNC:17867) is a protein-coding gene on chromosome 15q24.1, encoding Neuroplastin (Q9Y639). Probable homophilic and heterophilic cell adhesion molecule involved in long term potentiation at hippocampal excitatory synapses through activation of p38MAPK.

This gene encodes a type I transmembrane protein belonging to the Ig superfamily. The protein is believed to be involved in cell-cell interactions or cell-substrate interactions. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 27020 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 46 total — 4 pathogenic, 3 likely-pathogenic
• MANE Select transcript: NM_012428

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17867
Approved symbol	NPTN
Name	neuroplastin
Location	15q24.1
Locus type	gene with protein product
Status	Approved
Aliases	SDR1, GP55, GP65, np65, np55
Ensembl gene	ENSG00000156642
Ensembl biotype	protein_coding
OMIM	612820
Entrez	27020

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 17 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000345330, ENST00000351217, ENST00000561898, ENST00000562924, ENST00000563691, ENST00000563753, ENST00000564551, ENST00000565282, ENST00000565325, ENST00000567198, ENST00000916135, ENST00000916136, ENST00000916137, ENST00000970031, ENST00000970032, ENST00000970033, ENST00000970034, ENST00000970035, ENST00000970036, ENST00000970037

RefSeq mRNA: 4 — MANE Select: NM_012428 NM_001161363, NM_001161364, NM_012428, NM_017455

CCDS: CCDS10249, CCDS10250, CCDS58379, CCDS58380

Canonical transcript exons

ENST00000345330 — 9 exons

Exon	Start	End
ENSE00001110222	73563236	73563257
ENSE00001110230	73591966	73592137
ENSE00001304501	73570150	73570423
ENSE00001482662	73560014	73561048
ENSE00001863525	73633125	73633389
ENSE00003460821	73561896	73561970
ENSE00003533151	73587524	73587618
ENSE00003535274	73573662	73573795
ENSE00003628659	73597022	73597369

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 99.75.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 69.9980 / max 463.6289, expressed in 1820 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
150857	36.0529	1813
150856	29.6459	1800
150858	3.5570	1407
150855	0.4624	239
150854	0.2799	116

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
Brodmann (1909) area 23	UBERON:0013554	99.75	gold quality
lateral nuclear group of thalamus	UBERON:0002736	99.68	gold quality
cerebellar vermis	UBERON:0004720	99.56	gold quality
germinal epithelium of ovary	UBERON:0001304	99.53	gold quality
jejunal mucosa	UBERON:0000399	99.52	gold quality
cauda epididymis	UBERON:0004360	99.49	gold quality
bronchial epithelial cell	CL:0002328	99.48	gold quality
visceral pleura	UBERON:0002401	99.46	gold quality
blood vessel layer	UBERON:0004797	99.45	gold quality
esophagus squamous epithelium	UBERON:0006920	99.43	gold quality
adult organism	UBERON:0007023	99.43	gold quality
orbitofrontal cortex	UBERON:0004167	99.42	gold quality
caput epididymis	UBERON:0004358	99.42	gold quality
tibia	UBERON:0000979	99.41	gold quality
superior frontal gyrus	UBERON:0002661	99.41	gold quality
primary visual cortex	UBERON:0002436	99.40	gold quality
CA1 field of hippocampus	UBERON:0003881	99.39	gold quality
mucosa of sigmoid colon	UBERON:0004993	99.38	gold quality
corpus epididymis	UBERON:0004359	99.35	gold quality
seminal vesicle	UBERON:0000998	99.34	gold quality
substantia nigra pars compacta	UBERON:0001965	99.34	gold quality
palpebral conjunctiva	UBERON:0001812	99.33	gold quality
occipital lobe	UBERON:0002021	99.32	gold quality
postcentral gyrus	UBERON:0002581	99.31	gold quality
endothelial cell	CL:0000115	99.30	gold quality
middle temporal gyrus	UBERON:0002771	99.30	gold quality
pleura	UBERON:0000977	99.28	gold quality
parietal pleura	UBERON:0002400	99.28	gold quality
skin of hip	UBERON:0001554	99.25	gold quality
urethra	UBERON:0000057	99.24	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.56
E-HCAD-13	yes	7.82
E-MTAB-10137	yes	4.04

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

101 targeting NPTN, 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-513A-5P	100.00	69.77	2465
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-4715-3P	99.98	66.03	670
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-130A-3P	99.90	73.31	1861
HSA-MIR-130B-3P	99.90	73.27	1850
HSA-MIR-301A-3P	99.90	73.15	1839
HSA-MIR-301B-3P	99.90	73.19	1836
HSA-MIR-3666	99.90	73.24	1833

Literature-anchored findings (GeneRIF, showing 9)

• NPTN may be involved in genetic susceptibility to schizophrenia. (PMID:17123723)
• In human brain np65 is prominently present in cerebellum while np55 is the predominant isoform in mouse and rat cerebellum. (PMID:17196182)
• This study showed that Single nucleotide polymorphism in the neuroplastin locus associates with cortical thickness and intellectual ability in adolescents. (PMID:24514566)
• correct synaptic membrane protein localization, neuronal energy supply, expression of LTP and LTD, animal and human behaviour, and pathophysiology and disease–{review} (PMID:25040546)
• Xkr8-BSG/NPTN complex is required for phosphatidylserine scrambling in apoptotic cell membranes. (PMID:27503893)
• these results indicate that epilation induces McSCs activation through EDN3/EDNRB signaling and in turn leads to skin and hair hyperpigmentation. The findings suggest that EDN/EDNRB signaling may serve as a potential therapeutic target to promote repigmentation in hypopigmentation disorders. (PMID:28779130)
• Cryoelectron microscopy structure offers important insight into how the NPTN binds to the PMCA1. (PMID:30190470)
• Hippocampal expression of neuroplastin is altered in Alzheimer’s disease. (PMID:30488668)
• Expression profiling of NPTNbeta showed significantly high expression levels in lung cancer cell lines. NPTNbeta has strong ability to induce cancer-related cellular events, including anchorage-independent growth, motility and invasiveness, in lung cancer cells in response to extracellular S100A8/A9, eventually leading to the expression of a cancer disseminative phenotype in lung tissue in vivo. (PMID:30720226)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	nptnb	ENSDARG00000043864
danio_rerio	nptna	ENSDARG00000103002
mus_musculus	Nptn	ENSMUSG00000032336
rattus_norvegicus	Nptn	ENSRNOG00000009029
drosophila_melanogaster	Bsg	FBGN0261822
caenorhabditis_elegans		WBGENE00021305

Paralogs (3): VSTM2L (ENSG00000132821), EMB (ENSG00000170571), BSG (ENSG00000172270)

Protein

Protein identifiers

Neuroplastin — Q9Y639 (reviewed: Q9Y639)

Alternative names: Stromal cell-derived receptor 1

All UniProt accessions (4): Q9Y639, H3BQ94, H3BU51, Q9UFM8

UniProt curated annotations — full annotation on UniProt →

Function. Probable homophilic and heterophilic cell adhesion molecule involved in long term potentiation at hippocampal excitatory synapses through activation of p38MAPK. May also regulate neurite outgrowth by activating the FGFR1 signaling pathway. May play a role in synaptic plasticity. Also acts as a chaperone for ATP2B1; stabilizes ATP2B1 and increases its ATPase activity. Promotes localization of XKR8 at the cell membrane.

Subunit / interactions. Interacts with ATP2B1; this interaction stabilizes ATP2B1 and increases ATPase activity; this interaction controls T cell calcium homeostasis following T cell activation. Interacts with XKR8; promoting its localization at the cell membrane.

Subcellular location. Cell membrane Postsynaptic density.

Tissue specificity. Isoform 1 is ubiquitously expressed. Isoform 2 is expressed in brain cortex and cerebellum (at protein level).

Domain organisation. Some isoforms lack the first Ig-like domain which may confer homophilic adhesion activity. However, they can bind and activate FGFR1.

Isoforms (5)

UniProt ID	Names	Canonical?
Q9Y639-2	2, SDR-1-beta	yes
Q9Y639-1	1, SDR-1-alpha
Q9Y639-3	3
Q9Y639-4	4
Q9Y639-5	5

RefSeq proteins (4): NP_001154835, NP_001154836, NP_036560, NP_059429 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003598	Ig_sub2	Domain
IPR003599	Ig_sub	Domain
IPR007110	Ig-like_dom	Domain
IPR013098	Ig_I-set	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily

Pfam: PF07679, PF13927

UniProt features (23 total): glycosylation site 6, disulfide bond 3, splice variant 3, domain 3, topological domain 2, region of interest 2, signal peptide 1, chain 1, sequence conflict 1, transmembrane region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
6A69	ELECTRON MICROSCOPY	4.11

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y639-F1	87.08	0.73

Functional residue map

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

Disulfide bonds (3): 52–116, 170–218, 259–316

Glycosylation sites (6): 171, 197, 229, 284, 296, 317

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-977443	GABA receptor activation

MSigDB gene sets: 266 (showing top): GCM_MAP4K4, GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_GROWTH_FACTOR_STIMULUS, GOBP_NEURON_RECOGNITION, MORF_RAB5A, GOBP_REGULATION_OF_PHOSPHORYLATION, KAAB_FAILED_HEART_ATRIUM_DN, GOBP_SYNAPSE_ASSEMBLY, GOBP_REGULATION_OF_NEURONAL_SYNAPTIC_PLASTICITY, DITTMER_PTHLH_TARGETS_UP, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOCC_CELL_SURFACE, GOBP_NEUROGENESIS, GOBP_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, CTATGCA_MIR153, GOBP_POSITIVE_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT

GO Biological Process (19): negative regulation of cytokine production (GO:0001818), positive regulation of protein phosphorylation (GO:0001934), intracellular calcium ion homeostasis (GO:0006874), homophilic cell-cell adhesion (GO:0007156), positive regulation of cytosolic calcium ion concentration (GO:0007204), axon guidance (GO:0007411), positive regulation of neuron projection development (GO:0010976), positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743), positive regulation of long-term neuronal synaptic plasticity (GO:0048170), long-term synaptic potentiation (GO:0060291), dendrite self-avoidance (GO:0070593), regulation of receptor localization to synapse (GO:1902683), excitatory synapse assembly (GO:1904861), cell adhesion (GO:0007155), nervous system development (GO:0007399), modulation of chemical synaptic transmission (GO:0050804), synapse organization (GO:0050808), regulation of multicellular organismal process (GO:0051239), regulation of macromolecule metabolic process (GO:0060255)

GO Molecular Function (4): type 1 fibroblast growth factor receptor binding (GO:0005105), cell adhesion molecule binding (GO:0050839), cell-cell adhesion mediator activity (GO:0098632), protein binding (GO:0005515)

GO Cellular Component (9): immunological synapse (GO:0001772), plasma membrane (GO:0005886), cell surface (GO:0009986), postsynaptic density (GO:0014069), axon (GO:0030424), dendrite (GO:0030425), presynaptic membrane (GO:0042734), membrane (GO:0016020), synapse (GO:0045202)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Neurotransmitter receptors and postsynaptic signal transmission	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
cell-cell adhesion	2
neuron projection	2
cytokine production	1
regulation of cytokine production	1
negative regulation of gene expression	1
negative regulation of multicellular organismal process	1
regulation of protein phosphorylation	1
protein phosphorylation	1
positive regulation of protein modification process	1
positive regulation of phosphorylation	1
intracellular monoatomic cation homeostasis	1
calcium ion homeostasis	1
regulation of biological quality	1
axonogenesis	1
neuron projection guidance	1
regulation of neuron projection development	1
neuron projection development	1
positive regulation of cell projection organization	1
fibroblast growth factor receptor signaling pathway	1
positive regulation of signal transduction	1
regulation of fibroblast growth factor receptor signaling pathway	1
regulation of long-term neuronal synaptic plasticity	1
positive regulation of neurogenesis	1
regulation of synaptic plasticity	1
positive regulation of synaptic transmission	1
neuron recognition	1
regulation of localization	1
receptor localization to synapse	1
synapse assembly	1
cellular process	1
system development	1
chemical synaptic transmission	1
regulation of trans-synaptic signaling	1
cell junction organization	1
multicellular organismal process	1
regulation of biological process	1
regulation of metabolic process	1
macromolecule metabolic process	1
fibroblast growth factor receptor binding	1

Protein interactions and networks

STRING

1339 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NPTN	EPOR	P19235	990
NPTN	XKR8	Q9H6D3	696
NPTN	MANF	P55145	688
NPTN	BSG	P35613	652
NPTN	OAT	P04181	640
NPTN	ERVW-1	Q9UQF0	640
NPTN	USP5	P45974	639
NPTN	SPG21	Q9NZD8	635
NPTN	ATP2B1	P20020	620
NPTN	TPI1	P00938	588
NPTN	ATP2B2	Q01814	551
NPTN	GALC	P54803	495
NPTN	DIABLO	Q9NR28	492
NPTN	ITIH4	Q14624	476
NPTN	CYBA	P13498	464

IntAct

49 interactions, top by confidence:

A	B	Type	Score
TUBA1C	CCT6A	psi-mi:“MI:0914”(association)	0.640
PICK1	ILVBL	psi-mi:“MI:0914”(association)	0.530
LGALS3	PODXL	psi-mi:“MI:0914”(association)	0.530
FAM174A	BLTP3B	psi-mi:“MI:0914”(association)	0.530
ACTBL2	POTEF	psi-mi:“MI:0914”(association)	0.530
NPTN	TNPO2	psi-mi:“MI:0914”(association)	0.530
ARMC6	SLC27A2	psi-mi:“MI:0914”(association)	0.530
NPTN	NCAM1	psi-mi:“MI:0915”(physical association)	0.400
NPTN	AGTR1	psi-mi:“MI:0915”(physical association)	0.370
NPTN	SURF2	psi-mi:“MI:0915”(physical association)	0.370
	ESYT2	psi-mi:“MI:0914”(association)	0.350
MAD2L2		psi-mi:“MI:0914”(association)	0.350
M		psi-mi:“MI:0914”(association)	0.350
	NPC1	psi-mi:“MI:0914”(association)	0.350
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350
HCN1	POTEF	psi-mi:“MI:0914”(association)	0.350
ATP2B1	ACSL3	psi-mi:“MI:0914”(association)	0.350
CANX	HLA-A	psi-mi:“MI:0914”(association)	0.350
LGALS8	SLC22A23	psi-mi:“MI:0914”(association)	0.350
TUBB3	TUBB8B	psi-mi:“MI:0914”(association)	0.350
NPTN	RTL8C	psi-mi:“MI:0914”(association)	0.350
VAC14	NUDT19	psi-mi:“MI:0914”(association)	0.350
TUBA4A	NDUFA4	psi-mi:“MI:0914”(association)	0.350
DYNC2LI1	LAMP2	psi-mi:“MI:0914”(association)	0.350
GEMIN4	PHKA1	psi-mi:“MI:0914”(association)	0.350
DPH6	ATP2B2	psi-mi:“MI:0914”(association)	0.350
TNFAIP8L2	TES	psi-mi:“MI:0914”(association)	0.350

BioGRID (287): NPTN (Affinity Capture-MS), NPTN (Reconstituted Complex), NPTN (Affinity Capture-MS), NPTN (Proximity Label-MS), NPTN (Affinity Capture-MS), NPTN (Affinity Capture-MS), NPTN (Co-fractionation), NPTN (Co-fractionation), NPTN (Co-fractionation), NPTN (Co-fractionation), NPTN (Co-fractionation), NPTN (Co-fractionation), NPTN (Co-fractionation), NPTN (Co-fractionation), NPTN (Co-fractionation)

ESM2 similar proteins: A4IGL7, D3ZB51, E9PZ19, O75882, O94779, O95970, P00533, P02469, P07942, P13590, P15209, P24503, P24786, P33150, P39038, P55245, P55283, P68500, P97300, P97527, P97546, Q01279, Q01973, Q03351, Q16288, Q16620, Q1EGL2, Q3B7N0, Q3UQ28, Q5IFJ9, Q5IS37, Q5IS82, Q5R945, Q63604, Q6IS24, Q6VNS1, Q7TPD3, Q7TT15, Q8K4Y5, Q8N475

Diamond homologs: P17790, P18572, P26453, P35613, P97300, P97546, Q28740, Q6PCB8, Q6WRH9, Q865R3, Q99PA3, Q9Y639, O15394, O35158, O75325, Q32MD9, Q5VST9, P21995, Q9HCK4, O60469, Q5DTJ9, Q8VHZ8, Q91V87, Q9ERC8, A2A8L5, A7MBJ4, O02827, O75962, P10586, P23468, P29294, P56276, Q01974, Q15746, Q23551, Q28824, Q61006, Q64487, Q6PDN3, Q6PDS0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 73 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.

Reactome pathways:

Pathway	Partners	Fold	FDR
Activation of AMPK downstream of NMDARs	5	43.3×	2e-05
Recycling pathway of L1	6	30.5×	1e-05
Post NMDA receptor activation events	5	23.2×	1e-04
Activation of NMDA receptors and postsynaptic events	5	20.9×	1e-04
Autophagy	5	16.9×	2e-04
L1CAM interactions	6	16.4×	9e-05
PKR-mediated signaling	5	16.0×	3e-04
Interferon Signaling	5	13.7×	4e-04

GO biological processes:

GO term	Partners	Fold	FDR
amino acid transport	5	25.2×	1e-03
transport across blood-brain barrier	5	14.5×	8e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	4
Likely pathogenic	3
Uncertain significance	27
Likely benign	0
Benign	2

Top pathogenic / likely-pathogenic (7)

Variant ID	HGVS	Classification
3778807	NM_012428.4(NPTN):c.218_219del (p.Glu73fs)	Pathogenic
3778809	NM_012428.4(NPTN):c.342C>G (p.Tyr114Ter)	Pathogenic
3778810	NM_012428.4(NPTN):c.902del (p.Asn301fs)	Pathogenic
4819142	NM_012428.4(NPTN):c.409C>T (p.Arg137Ter)	Pathogenic
3778804	NM_012428.4(NPTN):c.403T>A (p.Trp135Arg)	Likely pathogenic
3778806	NM_012428.4(NPTN):c.1025C>T (p.Pro342Leu)	Likely pathogenic
3778808	NM_012428.4(NPTN):c.284C>G (p.Ser95Ter)	Likely pathogenic

SpliceAI

2305 predictions. Top by Δscore:

Variant	Effect	Δscore
15:73563285:CCA:C	acceptor_gain	1.0000
15:73563286:C:CT	acceptor_gain	1.0000
15:73563287:A:C	acceptor_gain	1.0000
15:73563294:A:AC	acceptor_gain	1.0000
15:73570144:TCTTA:T	donor_loss	1.0000
15:73570145:CTTA:C	donor_loss	1.0000
15:73570146:TTA:T	donor_loss	1.0000
15:73570147:TA:T	donor_loss	1.0000
15:73570148:A:AC	donor_gain	1.0000
15:73570149:C:CC	donor_gain	1.0000
15:73570149:C:CG	donor_loss	1.0000
15:73570149:CCGT:C	donor_gain	1.0000
15:73570419:ATGTC:A	acceptor_gain	1.0000
15:73570420:TGTC:T	acceptor_gain	1.0000
15:73570421:GTC:G	acceptor_gain	1.0000
15:73570422:TC:T	acceptor_gain	1.0000
15:73570423:CC:C	acceptor_gain	1.0000
15:73570424:C:CA	acceptor_loss	1.0000
15:73570424:C:CC	acceptor_gain	1.0000
15:73570425:T:C	acceptor_loss	1.0000
15:73570427:C:CT	acceptor_gain	1.0000
15:73570428:A:T	acceptor_gain	1.0000
15:73570434:G:C	acceptor_gain	1.0000
15:73570434:G:GC	acceptor_gain	1.0000
15:73573656:ACT:A	donor_loss	1.0000
15:73573658:TCA:T	donor_loss	1.0000
15:73573659:CA:C	donor_loss	1.0000
15:73573660:A:AC	donor_gain	1.0000
15:73573660:ACCA:A	donor_loss	1.0000
15:73573661:C:CA	donor_loss	1.0000

AlphaMissense

2617 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:73570206:A:T	L353H	1.000
15:73570272:A:G	L331P	1.000
15:73570316:A:C	C316W	1.000
15:73570317:C:G	C316S	1.000
15:73570318:A:G	C316R	1.000
15:73570318:A:T	C316S	1.000
15:73573689:C:A	W271C	1.000
15:73573689:C:G	W271C	1.000
15:73573691:A:G	W271R	1.000
15:73573691:A:T	W271R	1.000
15:73573727:A:G	C259R	1.000
15:73587578:A:G	C218R	1.000
15:73592027:A:G	W184R	1.000
15:73592027:A:T	W184R	1.000
15:73592069:A:G	C170R	1.000
15:73597043:C:G	A140P	1.000
15:73597056:C:A	W135C	1.000
15:73597056:C:G	W135C	1.000
15:73597058:A:G	W135R	1.000
15:73597058:A:T	W135R	1.000
15:73597108:G:T	A118D	1.000
15:73597110:C:A	R117S	1.000
15:73597110:C:G	R117S	1.000
15:73597113:G:C	C116W	1.000
15:73597114:C:A	C116F	1.000
15:73597114:C:G	C116S	1.000
15:73597114:C:T	C116Y	1.000
15:73597115:A:G	C116R	1.000
15:73597115:A:T	C116S	1.000
15:73597121:A:C	Y114D	1.000

dbSNP variants (sampled 300 via entrez): RS1000019149 (15:73631026 G>A), RS1000062040 (15:73613956 G>A), RS1000071454 (15:73630755 G>A), RS1000209300 (15:73613097 C>G,T), RS1000302405 (15:73623864 T>A,G), RS1000369512 (15:73570873 A>C), RS1000372613 (15:73581341 A>C), RS1000406410 (15:73588131 T>C), RS1000410931 (15:73563736 G>C), RS1000437518 (15:73587884 C>T), RS1000597736 (15:73605682 G>A), RS1000648878 (15:73618585 G>C), RS1000655200 (15:73618385 C>G), RS1000739804 (15:73586489 C>G), RS1000742363 (15:73631230 C>T)

Disease associations

OMIM: gene MIM:612820 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST004072_1	Cold medicine-related Stevens-Johnson syndrome/toxic epidermal necrolysis (SJS/TEN) with severe ocular complications	2.000000e-08
GCST005956_11	Waist-to-hip ratio adjusted for BMI	1.000000e-08
GCST005962_52	Waist-to-hip ratio adjusted for BMI x sex x age interaction (4df test)	5.000000e-07
GCST007277_20	Tourette syndrome	7.000000e-06

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0006997	response to cold medicine
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0008007	age at assessment
EFO:0008343	sex interaction measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	7
bisphenol F	increases expression, affects cotreatment	2
Benzo(a)pyrene	decreases methylation, increases mutagenesis	2
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, affects localization, increases expression	1
beta-lapachone	increases expression	1
potassium chromate(VI)	decreases expression	1
beta-methylcholine	affects expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
nutlin 3	affects cotreatment, increases secretion	1
bisphenol B	increases expression	1
LDN 193189	affects cotreatment, decreases expression	1
Antineoplastic Agents, Immunological	decreases response to substance, decreases expression	1
Arsenic Trioxide	increases expression	1
Aerosols	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Asbestos	affects methylation	1
Dactinomycin	increases secretion, affects cotreatment	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Furaldehyde	decreases expression, affects cotreatment, affects localization	1
Hydrogen Peroxide	affects expression	1
Indomethacin	increases expression, affects cotreatment	1
Ivermectin	decreases expression	1
Lead	increases expression	1
Methotrexate	decreases expression	1
Potassium Dichromate	increases expression	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B3CP	Abcam HEK293T NPTN KO	Transformed cell line	Female

Clinical trials (associated diseases)

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