NPTX1

Summary

NPTX1 (neuronal pentraxin 1, HGNC:7952) is a protein-coding gene on chromosome 17q25.3, encoding Neuronal pentraxin-1 (Q15818). May be involved in mediating uptake of synaptic material during synapse remodeling or in mediating the synaptic clustering of AMPA glutamate receptors at a subset of excitatory synapses.

NPTX1 is a member of the neuronal pentraxin gene family. Neuronal pentraxin 1 is similar to the rat NP1 gene which encodes a binding protein for the snake venom toxin taipoxin. Human NPTX1 mRNA is exclusively localized to the nervous system.

Source: NCBI Gene 4884 — RefSeq curated summary.

At a glance

• Gene–disease (curated): spinocerebellar ataxia 50 (Strong, GenCC) — +2 more curated relationships
• GWAS associations: 2
• Clinical variants (ClinVar): 68 total — 1 pathogenic, 4 likely-pathogenic
• Phenotypes (HPO): 20
• MANE Select transcript: NM_002522

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:7952
Approved symbol	NPTX1
Name	neuronal pentraxin 1
Location	17q25.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000171246
Ensembl biotype	protein_coding
OMIM	602367
Entrez	4884

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 2 protein_coding, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000306773, ENST00000535681, ENST00000571100, ENST00000575212, ENST00000695485

RefSeq mRNA: 1 — MANE Select: NM_002522 NM_002522

CCDS: CCDS32762

Canonical transcript exons

ENST00000306773 — 5 exons

Exon	Start	End
ENSE00001241399	80466834	80471034
ENSE00001293259	80476003	80476607
ENSE00003479456	80475511	80475718
ENSE00003594529	80471732	80471911
ENSE00003614692	80473200	80473444

Expression profiles

Bgee: expression breadth ubiquitous, 210 present calls, max score 99.82.

FANTOM5 (CAGE): breadth broad, TPM avg 4.0976 / max 273.9340, expressed in 466 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
168625	4.0976	466

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar vermis	UBERON:0004720	99.82	gold quality
paraflocculus	UBERON:0005351	99.15	gold quality
middle temporal gyrus	UBERON:0002771	98.91	gold quality
cerebellum	UBERON:0002037	98.77	gold quality
frontal pole	UBERON:0002795	98.74	gold quality
cerebellar cortex	UBERON:0002129	98.73	gold quality
cerebellar hemisphere	UBERON:0002245	98.72	gold quality
right hemisphere of cerebellum	UBERON:0014890	98.62	gold quality
parietal lobe	UBERON:0001872	98.08	gold quality
postcentral gyrus	UBERON:0002581	97.83	gold quality
superior frontal gyrus	UBERON:0002661	97.63	gold quality
Brodmann (1909) area 10	UBERON:0013541	97.51	gold quality
orbitofrontal cortex	UBERON:0004167	97.10	gold quality
occipital lobe	UBERON:0002021	96.99	gold quality
primary visual cortex	UBERON:0002436	96.76	gold quality
Brodmann (1909) area 46	UBERON:0006483	96.61	gold quality
Brodmann (1909) area 23	UBERON:0013554	96.50	gold quality
pons	UBERON:0000988	96.34	gold quality
frontal cortex	UBERON:0001870	95.82	gold quality
frontal lobe	UBERON:0016525	95.82	gold quality
entorhinal cortex	UBERON:0002728	95.77	gold quality
Brodmann (1909) area 9	UBERON:0013540	95.77	gold quality
prefrontal cortex	UBERON:0000451	95.73	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	95.37	gold quality
right frontal lobe	UBERON:0002810	95.10	gold quality
neocortex	UBERON:0001950	94.78	gold quality
cerebral cortex	UBERON:0000956	94.52	gold quality
stromal cell of endometrium	CL:0002255	94.22	gold quality
dorsal root ganglion	UBERON:0000044	94.18	gold quality
cingulate cortex	UBERON:0003027	93.71	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	41.09
E-MTAB-7316	yes	22.97
E-ANND-3	no	2.58

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ID3, IRX1, MYOD1, ZNF384

miRNA regulators (miRDB)

231 targeting NPTX1, 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-8485	100.00	77.57	4731
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-9-5P	100.00	72.28	2361
HSA-MIR-3163	100.00	77.23	8605
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-4673	100.00	66.64	1490
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-548AW	99.99	72.57	3559
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-8075	99.97	67.20	962
HSA-MIR-7152-3P	99.97	67.47	849

Literature-anchored findings (GeneRIF, showing 16)

• The purpose of the present study was to assess the toxic effect of taipoxin in SCLC-cell lines and to determine if toxicity correlates to NPR and NP1 and NP2 expression levels. (PMID:16115696)
• Neuronal pentraxin 1 transgene is a key factor for the synapse loss, the neurite damage, and the apoptotic neuronal death evoked by amyloid-beta protein, which regulates NP1 expression. (PMID:17151277)
• Long acting progestin contraceptive-enhanced NPTX1 secretion and reactive oxygen species generation in endometrial stromal cells impair endometrial endothelial cells survival resulting in a loss in vascular integrity. (PMID:25029423)
• NPTX1 was significantly associated with bipolar disorder. (PMID:25053281)
• Taken together, these results demonstrate that NP1 gene is a target of as hypoxia inducible factor-1 alpha and it regulates NP1 expression by binding to hypoxia responsive elements in its promoter region. (PMID:25498504)
• These results suggest that NPTX1 hypermethylation and consequent mRNA changes might be an important molecular mechanism in lung cancer. (PMID:25646694)
• findings suggest that lower NARP mRNA expression contributes to lower excitatory drive onto parvalbumin interneurons in schizophrenia. (PMID:26038830)
• NPTX1 is down-regulated in colon cancer. In addition, NPTX1 inhibits the proliferation of colon cancer cells via decreasing cyclin A2 and CDK2. (PMID:29345391)
• Relative to normal elderly, plasma NP1 was elevated in patients with mild cognitive impairment and elevated further in the subset that progressed to early-stage Alzheimer’s disease. (PMID:29501530)
• Findings indicate that neuronal pentraxin 1 (NPTX1) is a potential clinical therapeutic target. (PMID:31113871)
• MiR-4295 facilitates cell proliferation and metastasis in head and neck squamous cell carcinoma by targeting NPTX1. (PMID:31118494)
• Downregulation of NPTX1 induces cell cycle progression through Wnt/beta-catenin signaling in breast cancer. (PMID:34212686)
• NPTX1 mutations trigger endoplasmic reticulum stress and cause autosomal dominant cerebellar ataxia. (PMID:34788392)
• Tryptophan Metabolites Regulate Neuropentraxin 1 Expression in Endothelial Cells. (PMID:35216489)
• miR-148a-3p regulates proliferation and apoptosis of idiopathic gingival fibroma by targeting NPTX1. (PMID:37357360)
• Proteomic analysis of the human hippocampus identifies neuronal pentraxin 1 (NPTX1) as synapto-axonal target in late-stage Parkinson’s disease. (PMID:37515330)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	nptx1l	ENSDARG00000074671
mus_musculus	Nptx1	ENSMUSG00000025582
rattus_norvegicus	Nptx1	ENSRNOG00000003741

Paralogs (5): NPTX2 (ENSG00000106236), CRP (ENSG00000132693), APCS (ENSG00000132703), PTX3 (ENSG00000163661), PTX4 (ENSG00000251692)

Protein

Protein identifiers

Neuronal pentraxin-1 — Q15818 (reviewed: Q15818)

Alternative names: Neuronal pentraxin I

All UniProt accessions (2): A0A8Q3WL24, Q15818

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in mediating uptake of synaptic material during synapse remodeling or in mediating the synaptic clustering of AMPA glutamate receptors at a subset of excitatory synapses.

Subunit / interactions. Homooligomer or heterooligomer (probably pentamer) with neuronal pentraxin receptor (NPTXR).

Subcellular location. Secreted. Cytoplasmic vesicle. Secretory vesicle. Endoplasmic reticulum.

Disease relevance. Spinocerebellar ataxia 50 (SCA50) [MIM:620158] A form of spinocerebellar ataxia, a clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum with variable involvement of the brainstem and spinal cord. SCA50 is an autosomal dominant form characterized by cerebellar ataxia, oculomotor apraxia and other eye movement abnormalities, and cerebellar atrophy on brain imaging. The disease is caused by variants affecting the gene represented in this entry.

Cofactor. Binds 2 calcium ions per subunit.

RefSeq proteins (1): NP_002513* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001759	PTX_dom	Domain
IPR013320	ConA-like_dom_sf	Homologous_superfamily
IPR030476	Pentaxin_CS	Conserved_site
IPR051360	Neuronal_Pentraxin_Related	Family

Pfam: PF00354

UniProt features (43 total): strand 17, binding site 7, sequence variant 4, sequence conflict 4, helix 3, glycosylation site 2, signal peptide 1, chain 1, disulfide bond 1, domain 1, region of interest 1, turn 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
6YPE	X-RAY DIFFRACTION	1.45

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q15818-F1	76.75	0.46

Functional residue map

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

Ligand- & substrate-binding residues (7): 370; 280; 358; 358; 359; 360; 360

Disulfide bonds (1): 256–316

Glycosylation sites (2): 154, 193

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 326 (showing top): GGGACCA_MIR133A_MIR133B, MODY_HIPPOCAMPUS_POSTNATAL, BENPORATH_ES_WITH_H3K27ME3, MODULE_274, GOBP_SYNAPSE_ASSEMBLY, PEREZ_TP63_TARGETS, TTTGTAG_MIR520D, GCM_ZNF198, GOBP_CELLULAR_RESPONSE_TO_CARBOHYDRATE_STIMULUS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_RESPONSE_TO_POTASSIUM_ION, SCHLESINGER_METHYLATED_DE_NOVO_IN_CANCER, GOBP_NEUROGENESIS, CREBP1_Q2

GO Biological Process (9): mitochondrial transport (GO:0006839), chemical synaptic transmission (GO:0007268), central nervous system development (GO:0007417), cellular response to potassium ion (GO:0035865), mitochondrial fragmentation involved in apoptotic process (GO:0043653), axonogenesis involved in innervation (GO:0060385), cellular response to glucose stimulus (GO:0071333), postsynaptic density assembly (GO:0097107), neurotransmitter receptor localization to postsynaptic specialization membrane (GO:0099645)

GO Molecular Function (1): metal ion binding (GO:0046872)

GO Cellular Component (6): endoplasmic reticulum (GO:0005783), transport vesicle (GO:0030133), synaptic cleft (GO:0043083), glutamatergic synapse (GO:0098978), extracellular region (GO:0005576), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	2
endomembrane system	2
cellular anatomical structure	2
intracellular transport	1
anterograde trans-synaptic signaling	1
nervous system development	1
system development	1
response to potassium ion	1
cellular response to metal ion	1
apoptotic mitochondrial changes	1
axonogenesis	1
innervation	1
intracellular glucose homeostasis	1
response to glucose	1
cellular response to hexose stimulus	1
postsynaptic density organization	1
postsynaptic specialization assembly	1
excitatory synapse assembly	1
protein-containing complex localization	1
receptor localization to synapse	1
regulation of postsynaptic membrane neurotransmitter receptor levels	1
protein localization to postsynaptic specialization membrane	1
cation binding	1
intracellular membrane-bounded organelle	1
cytoplasmic vesicle	1
extracellular region	1
synapse	1
intracellular vesicle	1

Protein interactions and networks

STRING

1452 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NPTX1	SLITRK2	Q9H156	803
NPTX1	RCN2	Q14257	716
NPTX1	TBCD	Q9BTW9	666
NPTX1	OCA2	Q04671	649
NPTX1	HDC	P19113	648
NPTX1	IMMP2L	Q96T52	637
NPTX1	GRIA4	P48058	632
NPTX1	GRIA1	P42261	630
NPTX1	SLITRK1	Q96PX8	588
NPTX1	BAIAP2	Q9UQB8	577
NPTX1	SGCE	O43556	547
NPTX1	NPTXR	O95502	522
NPTX1	TOR1A	O14656	469
NPTX1	CCKBR	P32239	429
NPTX1	TDO2	P48775	429

IntAct

83 interactions, top by confidence:

A	B	Type	Score
SLC39A5	FAM171A2	psi-mi:“MI:0914”(association)	0.640
DEFA1	MANBA	psi-mi:“MI:0914”(association)	0.530
CHST10	B4GAT1	psi-mi:“MI:0914”(association)	0.530
IFI30	PRC1	psi-mi:“MI:0914”(association)	0.530
MMP10	TIMP1	psi-mi:“MI:0914”(association)	0.530
WNT7A	LDLR	psi-mi:“MI:0914”(association)	0.530
NAPSA	CTSD	psi-mi:“MI:0914”(association)	0.530
OGN	NPTX1	psi-mi:“MI:0914”(association)	0.530
	PLOD2	psi-mi:“MI:0914”(association)	0.530
ELSPBP1	PFDN1	psi-mi:“MI:0914”(association)	0.530
OS9	AGRN	psi-mi:“MI:0914”(association)	0.530
SIAE	NPTX1	psi-mi:“MI:0915”(physical association)	0.400
NPTX1	ADRB2	psi-mi:“MI:0915”(physical association)	0.370
Kif13b	TCF3	psi-mi:“MI:0914”(association)	0.350
PPP2CA	DKFZP586J0619	psi-mi:“MI:0914”(association)	0.350
TMEM132A	WWP2	psi-mi:“MI:0914”(association)	0.350
Wdr48	DMWD	psi-mi:“MI:0914”(association)	0.350
PRNP	WDR91	psi-mi:“MI:0914”(association)	0.350
WNT5A	POTEF	psi-mi:“MI:0914”(association)	0.350
CYB5D2	CBX6	psi-mi:“MI:0914”(association)	0.350
EPHA7	AGAP1	psi-mi:“MI:0914”(association)	0.350
TAZ	MANBA	psi-mi:“MI:0914”(association)	0.350
TCTN1	PPOX	psi-mi:“MI:0914”(association)	0.350
LYPD4	DPYSL4	psi-mi:“MI:0914”(association)	0.350
LYZL1	MANBA	psi-mi:“MI:0914”(association)	0.350
CD96	SQSTM1	psi-mi:“MI:0914”(association)	0.350
TM2D3	DDX39A	psi-mi:“MI:0914”(association)	0.350

BioGRID (113): NPTX1 (Affinity Capture-MS), NPTX1 (Affinity Capture-MS), NPTX1 (Affinity Capture-MS), NPTX1 (Affinity Capture-MS), NPTX1 (Affinity Capture-MS), NPTX1 (Affinity Capture-MS), NPTX1 (Affinity Capture-MS), NPTX1 (Affinity Capture-MS), NPTX1 (Affinity Capture-MS), NPTX1 (Affinity Capture-MS), NPTX1 (Affinity Capture-MS), NPTX1 (Affinity Capture-MS), NPTX1 (Affinity Capture-MS), NPTX1 (Affinity Capture-MS), NPTX1 (Affinity Capture-MS)

ESM2 similar proteins: A2AV25, A5PJQ2, A5PMY6, A6H6E2, B7ZNG0, O00548, O35764, O43278, O70340, O95502, P21757, P21758, P30204, P47970, P47971, P47972, P48759, P58660, P59900, P97738, Q05585, Q15818, Q24K15, Q2M1P5, Q5RFW0, Q61483, Q62443, Q6AZY7, Q6MG84, Q6ZMJ2, Q86VZ4, Q8BJS4, Q8C850, Q8CB67, Q8K299, Q8N539, Q8NI99, Q8R0Z6, Q95LU3, Q96NZ8

Diamond homologs: A0A1D5NSM8, A0JNA2, A2AVA0, A2AX52, D3YXF5, O02839, O19063, O35764, O43405, O70340, O76536, O89029, O95502, O96530, P02741, P02743, P06205, P06206, P06207, P06681, P07202, P07629, P08607, P09871, P0C6B8, P10643, P12246, P13944, P14151, P14847, P15697, P18337, P23680, P32018, P47970, P47971, P47972, P48199, P49254, P49262

SIGNOR signaling

10 interactions.

A	Effect	B	Mechanism
NPTX1	“up-regulates quantity”	BAD
NPTX1	“up-regulates quantity”	BAX
NPTX1	“down-regulates quantity”	BCL2
NPTX1	“down-regulates quantity”	MCL1
IRX1	“down-regulates quantity by repression”	NPTX1	“transcriptional regulation”
NPTX1	“up-regulates activity”	GRIA1	binding
Hypoxia	up-regulates	NPTX1
NPTX1	“up-regulates activity”	BAX	relocalization
NPTX1	“up-regulates activity”	BAD	relocalization
NPTX1	“up-regulates activity”	AMPA	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	4
Uncertain significance	52
Likely benign	6
Benign	2

Top pathogenic / likely-pathogenic (5)

Variant ID	HGVS	Classification
1806388	NM_002522.4(NPTX1):c.980A>G (p.Glu327Gly)	Pathogenic
1806389	NM_002522.4(NPTX1):c.428G>T (p.Arg143Leu)	Likely pathogenic
1806390	NM_002522.4(NPTX1):c.1109A>G (p.Gln370Arg)	Likely pathogenic
2692519	NM_002522.4(NPTX1):c.539G>T (p.Arg180Leu)	Likely pathogenic
3358966	NM_002522.4(NPTX1):c.1261_1287del (p.Thr421_Arg429del)	Likely pathogenic

SpliceAI

559 predictions. Top by Δscore:

Variant	Effect	Δscore
17:80471728:GTACC:G	donor_loss	1.0000
17:80471729:TACCT:T	donor_loss	1.0000
17:80471730:ACCTG:A	donor_loss	1.0000
17:80471731:CC:C	donor_loss	1.0000
17:80471731:CCTG:C	donor_gain	1.0000
17:80471757:C:CA	donor_gain	1.0000
17:80471907:GCCAC:G	acceptor_gain	1.0000
17:80471908:CCAC:C	acceptor_gain	1.0000
17:80471908:CCACC:C	acceptor_gain	1.0000
17:80471909:CAC:C	acceptor_gain	1.0000
17:80471909:CACC:C	acceptor_gain	1.0000
17:80471910:AC:A	acceptor_gain	1.0000
17:80471910:ACCTG:A	acceptor_loss	1.0000
17:80471911:CC:C	acceptor_gain	1.0000
17:80471911:CCT:C	acceptor_loss	1.0000
17:80471912:C:CC	acceptor_gain	1.0000
17:80471913:T:A	acceptor_loss	1.0000
17:80473195:TCTAC:T	donor_loss	1.0000
17:80473196:CTACC:C	donor_loss	1.0000
17:80473197:TACCT:T	donor_loss	1.0000
17:80473198:ACC:A	donor_loss	1.0000
17:80475505:CAGTA:C	donor_loss	1.0000
17:80475506:AGTAC:A	donor_loss	1.0000
17:80475507:GTAC:G	donor_loss	1.0000
17:80475508:TA:T	donor_loss	1.0000
17:80475509:A:AG	donor_loss	1.0000
17:80475510:CCTTT:C	donor_gain	1.0000
17:80470796:AG:A	donor_gain	0.9900
17:80470806:G:A	donor_gain	0.9900
17:80471032:GTCC:G	acceptor_loss	0.9900

AlphaMissense

2816 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:80470885:C:A	W409C	1.000
17:80470885:C:G	W409C	1.000
17:80470887:A:G	W409R	1.000
17:80470887:A:T	W409R	1.000
17:80471014:A:C	F366L	1.000
17:80471014:A:T	F366L	1.000
17:80471016:A:G	F366L	1.000
17:80471732:C:A	Q359H	1.000
17:80471732:C:G	Q359H	1.000
17:80471742:C:T	G356D	1.000
17:80471743:C:G	G356R	1.000
17:80471833:A:G	W326R	1.000
17:80471833:A:T	W326R	1.000
17:80471838:C:A	G324V	1.000
17:80471838:C:T	G324E	1.000
17:80471839:C:A	G324W	1.000
17:80471852:C:A	W319C	1.000
17:80471852:C:G	W319C	1.000
17:80471854:A:G	W319R	1.000
17:80471854:A:T	W319R	1.000
17:80471861:A:C	C316W	1.000
17:80471863:A:G	C316R	1.000
17:80471873:C:A	W312C	1.000
17:80471873:C:G	W312C	1.000
17:80471875:A:G	W312R	1.000
17:80471875:A:T	W312R	1.000
17:80473213:A:G	L295P	1.000
17:80473246:A:G	L284P	1.000
17:80476202:A:G	L82P	1.000
17:80470966:C:A	W382C	0.999

dbSNP variants (sampled 300 via entrez): RS1000185253 (17:80466415 C>A,T), RS1000196794 (17:80466570 C>T), RS1000239148 (17:80476703 G>C,T), RS1000355397 (17:80476587 C>A,T), RS1000358732 (17:80477638 C>A), RS1000424767 (17:80471641 C>A,T), RS1000547416 (17:80468186 A>C), RS1000709577 (17:80472581 C>A,G,T), RS1001110246 (17:80477487 CGCGCCCGGTATCCCCG>C), RS1001172442 (17:80477903 C>T), RS1001313342 (17:80472060 A>C), RS1001694553 (17:80471564 T>C), RS1001700696 (17:80472268 A>C,G), RS1001703036 (17:80477000 A>C), RS1001883706 (17:80477714 G>A,C)

Disease associations

OMIM: gene MIM:602367 | disease phenotypes: MIM:620158

GenCC curated gene-disease

Disease	Classification	Inheritance
spinocerebellar ataxia 50	Strong	Autosomal dominant
cerebellar ataxia	Strong	Autosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
autosomal dominant cerebellar ataxia	Limited	AD

Mondo (2): spinocerebellar ataxia 50 (MONDO:0859334), cerebellar ataxia (MONDO:0000437)

Orphanet (0):

HPO phenotypes

20 total (20 of 20 shown, HPO-id order):

HPO	Term
HP:0000006	Autosomal dominant inheritance
HP:0000365	Hearing impairment
HP:0000508	Ptosis
HP:0000639	Nystagmus
HP:0000651	Diplopia
HP:0001251	Ataxia
HP:0001272	Cerebellar atrophy
HP:0001336	Myoclonus
HP:0002072	Chorea
HP:0002174	Postural tremor
HP:0002186	Apraxia
HP:0002345	Action tremor
HP:0002346	Head tremor
HP:0002354	Memory impairment
HP:0003584	Late onset
HP:0003596	Middle age onset
HP:0006855	Cerebellar vermis atrophy
HP:0011462	Young adult onset
HP:0032121	Froment sign
HP:0033051	Impaired executive functioning

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST006585_1317	Blood protein levels	2.000000e-18
GCST008103_59	Bipolar disorder	5.000000e-07

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D002524	Cerebellar Ataxia	C10.228.140.252.190; C10.597.350.090.500; C23.888.592.350.090.200

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Particulate Matter	affects cotreatment, affects expression, decreases expression, increases abundance, increases expression	5
Valproic Acid	affects expression, increases expression, increases methylation	4
bisphenol A	decreases expression, increases expression	3
Benzo(a)pyrene	affects methylation, decreases expression, increases methylation, increases mutagenesis	3
entinostat	increases expression, affects cotreatment	2
Air Pollutants	increases abundance, increases expression	2
Cisplatin	affects expression, increases expression	2
Oxygen	increases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tetrachlorodibenzodioxin	affects reaction, increases expression	2
Tobacco Smoke Pollution	increases expression	2
p-Chloromercuribenzoic Acid	decreases expression, affects cotreatment	2
aristolochic acid I	increases expression	1
sotorasib	affects cotreatment, decreases expression	1
propionaldehyde	increases expression	1
lead acetate	decreases expression	1
2,5,2’,5’-tetrachlorobiphenyl	decreases expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
hydroxyhydroquinone	decreases expression	1
sulforaphane	decreases expression	1
boron nitride	decreases expression	1
butyraldehyde	increases expression	1
tetrabromobisphenol A	decreases expression	1
3,4,5,3’,4’-pentachlorobiphenyl	increases expression	1
zinc chromate	decreases expression, increases abundance	1
ferrous chloride	decreases expression	1
aflatoxin B2	increases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression	1
isobutyl alcohol	increases abundance, increases expression, affects cotreatment	1
mercuric bromide	affects cotreatment, decreases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B1YX	Abcam HeLa NPTX1 KO	Cancer cell line	Female
CVCL_D1TR	Abcam U-87MG NPTX1 KO	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00950196	PHASE4	COMPLETED	Amantadine for Improving Neurologic Symptoms in Ataxia-Telangiectasia
NCT04107740	PHASE4	COMPLETED	C-Trelin Orally Disintegrated(OD) Tablet 5mg in Ataxia Due to Spinocerebellar Degeneration
NCT01970098	PHASE3	COMPLETED	A Confirmatory Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT01970111	PHASE3	COMPLETED	An Extension Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT01970124	PHASE3	COMPLETED	A Long-Term Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT01970137	PHASE3	COMPLETED	A 24-week Open-label Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT02889302	PHASE3	COMPLETED	An Additional Confirmatory Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT03408080	PHASE3	ACTIVE_NOT_RECRUITING	Open Pilot Trial of BHV-4157
NCT03701399	PHASE3	ACTIVE_NOT_RECRUITING	Troriluzole in Adult Participants With Spinocerebellar Ataxia
NCT03901638	PHASE3	TERMINATED	Tllsh2910 for Ataxia and Gut Microbiota Alteration in Patients of Multiple System Atrophy
NCT07040137	PHASE3	RECRUITING	Confirmatory Study 3 of KPS-0373 in Patients With Spinocerebellar Degeneration
NCT00034242	PHASE2	COMPLETED	High-Dose Intravenous Immunoglobulin to Treat Cerebellar Degeneration
NCT00202397	PHASE2	COMPLETED	Effect of Riluzole as a Symptomatic Approach in Patients With Chronic Cerebellar Ataxia
NCT00863538	PHASE2	COMPLETED	Phase II Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT01004016	PHASE2	COMPLETED	A Study of KPS-0373 in Patients With Spinocerebellar Degeneration (SCD)
NCT01350440	PHASE2	COMPLETED	Safety and Efficacy of Intravenous Immune Globulin in Treating Spinocerebellar Ataxia
NCT02540655	PHASE2	COMPLETED	Efficacy and Safety Study of Stemchymal® in Polyglutamine Spinocerebellar Ataxia
NCT03932669	PHASE2	COMPLETED	Effect of Nilotinib in Cerebellar Ataxia Patients
NCT04301284	PHASE2	WITHDRAWN	Study of CAD-1883 for Spinocerebellar Ataxia
NCT05125666	PHASE2	UNKNOWN	Efficacy of Dual Task Training on Children With Ataxia After Medulloblastoma Resection
NCT06397274	PHASE2	NOT_YET_RECRUITING	Stemchymal® for Polyglutamine Spinocerebellar Ataxia
NCT00683943	PHASE1	COMPLETED	Lithium Treatment for Patients With Spinocerebellar Ataxia Type I
NCT02287064	PHASE1	UNKNOWN	An Open-label Trial of Intravenous Immune Globulin (IVIG)in Treating Spinocerebellar Ataxias
NCT05157802	PHASE1	ACTIVE_NOT_RECRUITING	Promoting Physical Activity Engagement for People With Early-stage Cerebellar Ataxia
NCT01104649	PHASE2/PHASE3	COMPLETED	Efficacy of Riluzole in Hereditary Cerebellar Ataxia
NCT02960893	PHASE2/PHASE3	COMPLETED	Trial in Adult Participants With Spinocerebellar Ataxia (SCA)
NCT00244361	PHASE1/PHASE2	COMPLETED	Effectiveness of Rituximab in Pediatric OMS Patients.
NCT01649687	PHASE1/PHASE2	COMPLETED	Treatment of Cerebellar Ataxia With Mesenchymal Stem Cells
NCT01958177	PHASE1/PHASE2	UNKNOWN	Clinical Study to Evaluate the Safety and Efficacy BMMNC in Cerebellar Ataxia
NCT02829268	PHASE1/PHASE2	COMPLETED	A Clinical Trial of Dantrolene Sodium in Pediatric and Adult Patients With Wolfram Syndrome
NCT00001324	Not specified	COMPLETED	PET Scan to Study Brain Control of Human Movement
NCT00006492	Not specified	COMPLETED	Gluten-Free Diet in Patients With Gluten Sensitivity and Cerebellar Ataxia
NCT00136630	Not specified	COMPLETED	Natural History, Genetic Bases and Phenotype-genotype Correlations in Autosomal Dominant Spinocerebellar Degenerations
NCT00140829	Not specified	COMPLETED	SPATAX: Clinical and Genetic Analysis of Cerebellar Ataxias and Spastic Paraplegias
NCT00272272	Not specified	COMPLETED	Fall Prevention in a Geriatric Nursing Home Setting Using the Music of Nolwenn Leroy
NCT00654251	Not specified	COMPLETED	Measuring Neurological Impairment and Functional Visual Assessment In Spinocerebellar Ataxias
NCT00692861	Not specified	COMPLETED	Autoimmunity in Neurologic Complications of Celiac Disease
NCT01037777	Not specified	COMPLETED	RISCA : Prospective Study of Individuals at Risk for SCA1, SCA2, SCA3, SCA6, SCA7
NCT01307176	Not specified	COMPLETED	Exercise Training Program for Cerebellar Ataxia
NCT01428531	Not specified	COMPLETED	Special Drug Use Investigation for Arixtra® (Fondaparinux) Venous Thromboembolism Treatment