NIPSNAP1

Summary

NIPSNAP1 (nipsnap homolog 1, HGNC:7827) is a protein-coding gene on chromosome 22q12.2, encoding Protein NipSnap homolog 1 (Q9BPW8). Protein involved in mitophagy by facilitating recruitment of the autophagy machinery required for clearance of damaged mitochondria.

This gene encodes a member of the NipSnap family of proteins that may be involved in vesicular transport. A similar protein in mice inhibits the calcium channel TRPV6, and is also localized to the inner mitochondrial membrane where it may play a role in mitochondrial DNA maintenance. A pseudogene of this gene is located on the short arm of chromosome 17. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene.

Source: NCBI Gene 8508 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 40 total
• Druggable target: yes
• MANE Select transcript: NM_003634

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:7827
Approved symbol	NIPSNAP1
Name	nipsnap homolog 1
Location	22q12.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000184117
Ensembl biotype	protein_coding
OMIM	603249
Entrez	8508

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 10 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000216121, ENST00000415100, ENST00000437094, ENST00000455496, ENST00000494966, ENST00000496944, ENST00000880436, ENST00000880437, ENST00000880438, ENST00000880439, ENST00000880440, ENST00000937731, ENST00000937732

RefSeq mRNA: 2 — MANE Select: NM_003634 NM_001202502, NM_003634

CCDS: CCDS13860

Canonical transcript exons

ENST00000216121 — 10 exons

Exon	Start	End
ENSE00000652086	29558870	29558953
ENSE00000652087	29560734	29560828
ENSE00000652089	29561506	29561646
ENSE00001309149	29554808	29555999
ENSE00001701004	29561171	29561202
ENSE00001878960	29580985	29581113
ENSE00003487397	29570405	29570532
ENSE00003518111	29569193	29569287
ENSE00003540524	29561792	29561862
ENSE00003577900	29570162	29570207

Expression profiles

Bgee: expression breadth ubiquitous, 280 present calls, max score 97.76.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 28.4179 / max 265.3471, expressed in 1774 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
193544	28.4179	1774

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	97.76	gold quality
cortical plate	UBERON:0005343	97.73	gold quality
embryo	UBERON:0000922	97.61	gold quality
ganglionic eminence	UBERON:0004023	97.56	gold quality
liver	UBERON:0002107	97.18	gold quality
renal medulla	UBERON:0000362	96.15	gold quality
lateral nuclear group of thalamus	UBERON:0002736	95.98	gold quality
ventricular zone	UBERON:0003053	95.96	gold quality
adult mammalian kidney	UBERON:0000082	95.85	gold quality
olfactory bulb	UBERON:0002264	95.72	silver quality
type B pancreatic cell	CL:0000169	95.71	silver quality
substantia nigra pars compacta	UBERON:0001965	95.71	gold quality
cervix squamous epithelium	UBERON:0006922	95.48	silver quality
substantia nigra pars reticulata	UBERON:0001966	95.21	gold quality
right adrenal gland	UBERON:0001233	95.09	gold quality
lateral globus pallidus	UBERON:0002476	94.97	gold quality
cerebellar vermis	UBERON:0004720	94.97	gold quality
right adrenal gland cortex	UBERON:0035827	94.97	gold quality
prefrontal cortex	UBERON:0000451	94.89	gold quality
adrenal tissue	UBERON:0018303	94.80	gold quality
pons	UBERON:0000988	94.64	gold quality
pancreatic ductal cell	CL:0002079	94.52	silver quality
middle temporal gyrus	UBERON:0002771	94.41	gold quality
tongue squamous epithelium	UBERON:0006919	94.30	silver quality
kidney	UBERON:0002113	94.29	gold quality
islet of Langerhans	UBERON:0000006	94.25	gold quality
superior vestibular nucleus	UBERON:0007227	94.25	gold quality
right frontal lobe	UBERON:0002810	94.20	gold quality
nucleus accumbens	UBERON:0001882	94.10	gold quality
cingulate cortex	UBERON:0003027	94.10	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-HCAD-10	yes	16.60
E-ANND-3	yes	8.99
E-GEOD-36552	no	153.35

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

66 targeting NIPSNAP1, 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-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-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-12118	100.00	65.88	1270
HSA-MIR-1193	100.00	65.93	529
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-433-3P	99.98	69.37	1203
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-4493	99.90	66.48	977
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-202-3P	99.84	71.41	1290
HSA-MIR-6515-3P	99.82	68.19	1933
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-548AU-3P	99.70	68.22	1373
HSA-MIR-4530	99.69	66.47	1509
HSA-MIR-6883-5P	99.69	68.05	3785

Literature-anchored findings (GeneRIF, showing 9)

• This study presents the first physiological function of mouse Nipsnap1 as an associated protein inhibiting transient receptor potential vanilloid channel 6 activity that possibly exerts its effect directly at the plasma membrane. (PMID:18392847)
• NIPSNAP1 is an interacting molecule of NST and plays a crucial role in pain transmission. (PMID:22311985)
• Structural variants unique to the malignant cell line inactivated: gene NIPSNAP1, putative tumor suppressor that inhibits TRPV6, an anti-apoptotic oncogene implicated in prostate cancer progression. (PMID:23792589)
• NIPSNAP1 mutations could not explain phenotype of patients with combined oxidative phosphorylation system deficiencies. (PMID:24137763)
• These results suggest that changes in NIPSNAP1 expression may contribute to the pathogenesis of inflammatory pain. (PMID:27030720)
• identified mitochondrial proteins 4-nitrophenylphosphatase domain and non-neuronal synaptosomal associated protein 25-like protein homolog (NIP-SNAP)-1 and -2 as clarithromycin-binding proteins. Production of proinflammatory cytokines induced by lipopolysaccharides and Pam3-CSK4 in epithelial cell lines BEAS-2B and T24 were suppressed by knockdown of NIP-SNAP-1 or -2 (PMID:27998764)
• NIP-SNAP-1 and -2 localized in the mitochondrial inner membrane space, whereas HSP60 localized in the matrix. Expression levels of NIP-SNAP-1 and -2 in cells were decreased by knockdown of HSP60, but not HSP10. The findings indicate that HSP60 promotes folding and maintains the stability of NIP-SNAP-1 and -2. (PMID:28011268)
• NIPSNAP1 and NIPSNAP2 have a redundant function in mitophagy and are predominantly expressed in different tissues. (PMID:30982665)
• The Tumorigenic Effect of lncRNA AFAP1-AS1 is Mediated by Translated Peptide ATMLP Under the Control of m[6] A Methylation. (PMID:36871154)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	nipsnap1	ENSDARG00000005320
mus_musculus	Nipsnap1	ENSMUSG00000034285
rattus_norvegicus	Nipsnap1	ENSRNOG00000008374
drosophila_melanogaster	Nipsnap	FBGN0030724
caenorhabditis_elegans		WBGENE00019301

Paralogs (3): NIPSNAP3A (ENSG00000136783), NIPSNAP2 (ENSG00000146729), NIPSNAP3B (ENSG00000165028)

Protein

Protein identifiers

Protein NipSnap homolog 1 — Q9BPW8 (reviewed: Q9BPW8)

All UniProt accessions (4): C9JDV8, Q9BPW8, F8WCR5, H7C2U6

UniProt curated annotations — full annotation on UniProt →

Function. Protein involved in mitophagy by facilitating recruitment of the autophagy machinery required for clearance of damaged mitochondria. Accumulates on the mitochondria surface in response to mitochondrial depolarization and acts as a ’eat me’ signal by recruiting proteins involved in selective autophagy, such as autophagy receptors (CALCOCO2/NDP52, NBR1, SQSTM1/p62, TAX1BP1 and WDFY3/ALFY) and ATG8 family proteins (MAP1LC3A, MAP1LC3B, MAP1LC3C, GABARAP, GABARAPL1 and GABARAPL2).

Subunit / interactions. Interacts with CALCOCO2/NDP52, NBR1, SQSTM1/p62, TAX1BP1 and WDFY3/ALFY. Interacts with ATG8 family proteins (MAP1LC3A, MAP1LC3B, MAP1LC3C, GABARAP, GABARAPL1 and GABARAPL2).

Subcellular location. Mitochondrion matrix.

Tissue specificity. Ubiquitous. Highest expression in liver.

Post-translational modifications. In response to mitochondrial stress, the precursor protein is ubiquitinated by the SIFI complex in the cytoplasm before mitochondrial import, leading to its degradation. Within the SIFI complex, UBR4 initiates ubiquitin chain that are further elongated or branched by KCMF1.

Similarity. Belongs to the NipSnap family.

RefSeq proteins (2): NP_001189431, NP_003625* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011008	Dimeric_a/b-barrel	Homologous_superfamily
IPR012577	NIPSNAP	Domain
IPR051557	NipSnap_domain	Family

Pfam: PF07978

UniProt features (17 total): modified residue 12, transit peptide 1, chain 1, sequence variant 1, sequence conflict 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BPW8-F1	83.50	0.69

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 (12): 146, 191, 193, 193, 279, 65, 66, 73, 80, 129, 143, 146

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 152 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, TGACCTY_ERR1_Q2, GOBP_MACROAUTOPHAGY, GOBP_SENSORY_PERCEPTION_OF_PAIN, HNF4_01, DODD_NASOPHARYNGEAL_CARCINOMA_UP, WANG_TARGETS_OF_MLL_CBP_FUSION_DN, GOBP_SENSORY_PERCEPTION, AFFAR_YY1_TARGETS_DN, WONG_MITOCHONDRIA_GENE_MODULE, CUI_TCF21_TARGETS_2_UP, PARENT_MTOR_SIGNALING_UP, CHIBA_RESPONSE_TO_TSA, NUYTTEN_EZH2_TARGETS_DN

GO Biological Process (3): mitophagy (GO:0000423), sensory perception of pain (GO:0019233), autophagy (GO:0006914)

GO Molecular Function (2): protein-macromolecule adaptor activity (GO:0030674), protein binding (GO:0005515)

GO Cellular Component (4): mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759), synaptic membrane (GO:0097060), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
autophagy of mitochondrion	1
macroautophagy	1
sensory perception	1
catabolic process	1
transmembrane transport	1
process utilizing autophagic mechanism	1
protein binding	1
molecular adaptor activity	1
binding	1
cytoplasm	1
intracellular membrane-bounded organelle	1
mitochondrion	1
intracellular organelle lumen	1
synapse	1
plasma membrane region	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1168 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NIPSNAP1	TRPV6	Q9H1D0	860
NIPSNAP1	TRPV5	Q9NQA5	835
NIPSNAP1	THOC5	Q13769	781
NIPSNAP1	SNAP25	P13795	732
NIPSNAP1	TAX1BP1	Q86VP1	721
NIPSNAP1	GABARAPL2	P60520	719
NIPSNAP1	F5GZY7	F5GZY7	708
NIPSNAP1	CALCOCO2	Q13137	708
NIPSNAP1	NBR1	Q14596	682
NIPSNAP1	BNIP3L	O60238	617
NIPSNAP1	GABARAP	O95166	585
NIPSNAP1	SQSTM1	Q13501	582
NIPSNAP1	PINK1	Q9BXM7	532
NIPSNAP1	BNIP3	Q12983	529
NIPSNAP1	FUNDC1	Q8IVP5	514

IntAct

115 interactions, top by confidence:

A	B	Type	Score
WDR19	TULP3	psi-mi:“MI:0914”(association)	0.860
CTTNBP2NL	STRN	psi-mi:“MI:2364”(proximity)	0.820
NDUFS3	NDUFS8	psi-mi:“MI:0914”(association)	0.730
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
HSPD1	NUDT19	psi-mi:“MI:0914”(association)	0.710
GABARAPL2	IPO5	psi-mi:“MI:0914”(association)	0.690
SQSTM1	NIPSNAP1	psi-mi:“MI:0915”(physical association)	0.650
KLHL22	TMEM223	psi-mi:“MI:0914”(association)	0.640
NIPSNAP2	HSPD1	psi-mi:“MI:0914”(association)	0.610
GABARAPL1	IPO5	psi-mi:“MI:0914”(association)	0.590
RGS2	NIPSNAP1	psi-mi:“MI:0915”(physical association)	0.550
PRKCI	NIPSNAP2	psi-mi:“MI:0914”(association)	0.530
PRKCZ	IPO5	psi-mi:“MI:0914”(association)	0.530
EBNA-LP	HAX1	psi-mi:“MI:0914”(association)	0.530
MAP1LC3B	NIPSNAP2	psi-mi:“MI:0914”(association)	0.520
IFT140	ACSL3	psi-mi:“MI:0914”(association)	0.510
CDH1	ACTN4	psi-mi:“MI:0914”(association)	0.500
GPC1	SNAP23	psi-mi:“MI:0915”(physical association)	0.400
GPC1	GANAB	psi-mi:“MI:0915”(physical association)	0.400
	NIPSNAP1	psi-mi:“MI:0915”(physical association)	0.370
NIPSNAP1	E6	psi-mi:“MI:0915”(physical association)	0.370
DBI	NIPSNAP1	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (298): NIPSNAP1 (Affinity Capture-RNA), NIPSNAP1 (Affinity Capture-RNA), NIPSNAP1 (Affinity Capture-RNA), NIPSNAP1 (Affinity Capture-RNA), NIPSNAP1 (Affinity Capture-MS), NIPSNAP1 (Affinity Capture-MS), NIPSNAP1 (Affinity Capture-MS), NIPSNAP1 (Affinity Capture-MS), NIPSNAP1 (Affinity Capture-MS), NIPSNAP1 (Affinity Capture-MS), NIPSNAP1 (Affinity Capture-MS), NIPSNAP1 (Proximity Label-MS), NIPSNAP1 (Affinity Capture-MS), CCT6A (Affinity Capture-MS), FAT1 (Affinity Capture-MS)

ESM2 similar proteins: A0A063C1W0, A0A2I1C3W7, A0A5B8YU67, A2BGU9, B3P9N0, B4I9J6, B4PY69, B4R313, B8DH02, B9DKR5, B9FK36, C1KX66, E1ACR2, F4I1L3, F6NVH9, I1RVD6, O46084, O55125, O55126, O75323, P27680, P34492, P91929, Q09422, Q16KN5, Q19000, Q29JQ0, Q4WAZ2, Q502L2, Q54I58, Q562B5, Q5FWM4, Q61CA3, Q6C3P4, Q71XQ0, Q8BX10, Q8IQ70, Q8S6N5, Q8SYD0, Q8Y5F1

Diamond homologs: F6NVH9, O55125, O55126, O75323, P34492, Q9BPW8, Q9PU58, Q9VXK0, A6NDG6, D3ZDK7, P0DKC3, P0DKC4, P19881, P60487, Q00472, Q2T9S4, Q3ZBF9, Q5F4B1, Q6ZT62, Q8CHP8, Q8GWU0, Q8VD52, Q96GD0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 105 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
Selective autophagy	5	20.2×	9e-04
Macroautophagy	8	13.4×	6e-05
Autophagy	5	10.8×	7e-03
Fatty acid metabolism	5	9.5×	8e-03

GO biological processes:

GO term	Partners	Fold	FDR
mitophagy	7	25.3×	5e-06
autophagosome maturation	6	23.9×	5e-05
macroautophagy	5	13.7×	6e-03
autophagosome assembly	5	12.8×	6e-03
autophagy	7	8.8×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	23
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1342 predictions. Top by Δscore:

Variant	Effect	Δscore
22:29555995:GGGGA:G	acceptor_gain	1.0000
22:29556000:C:CC	acceptor_gain	1.0000
22:29558865:CTCA:C	donor_loss	1.0000
22:29558866:TCAC:T	donor_loss	1.0000
22:29558867:CACCT:C	donor_loss	1.0000
22:29558868:A:AC	donor_gain	1.0000
22:29558868:A:AT	donor_loss	1.0000
22:29558869:C:CA	donor_loss	1.0000
22:29558869:C:CC	donor_gain	1.0000
22:29558949:ATAGG:A	acceptor_gain	1.0000
22:29558950:TAGG:T	acceptor_gain	1.0000
22:29558951:AGG:A	acceptor_gain	1.0000
22:29558951:AGGC:A	acceptor_loss	1.0000
22:29558952:GG:G	acceptor_gain	1.0000
22:29558953:GC:G	acceptor_loss	1.0000
22:29558954:C:CC	acceptor_gain	1.0000
22:29561169:A:AC	donor_gain	1.0000
22:29561170:C:CC	donor_gain	1.0000
22:29561517:ATGT:A	donor_gain	1.0000
22:29561520:T:TA	donor_gain	1.0000
22:29561526:G:C	donor_gain	1.0000
22:29561644:CTC:C	acceptor_gain	1.0000
22:29561644:CTCCT:C	acceptor_loss	1.0000
22:29561646:CCTG:C	acceptor_loss	1.0000
22:29561647:CT:C	acceptor_loss	1.0000
22:29561859:TGCA:T	acceptor_gain	1.0000
22:29561861:CA:C	acceptor_gain	1.0000
22:29561863:C:CC	acceptor_gain	1.0000
22:29569188:CTTAC:C	donor_loss	1.0000
22:29569189:TTACC:T	donor_loss	1.0000

AlphaMissense

1856 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
22:29558892:C:A	W256C	1.000
22:29558892:C:G	W256C	1.000
22:29558894:A:G	W256R	1.000
22:29558894:A:T	W256R	1.000
22:29558909:A:G	W251R	1.000
22:29558909:A:T	W251R	1.000
22:29560737:A:G	W235R	1.000
22:29560737:A:T	W235R	1.000
22:29561182:C:A	W200C	1.000
22:29561182:C:G	W200C	1.000
22:29561184:A:G	W200R	1.000
22:29561184:A:T	W200R	1.000
22:29561198:C:T	G195E	1.000
22:29561525:A:G	L187P	1.000
22:29561568:A:G	W173R	1.000
22:29561568:A:T	W173R	1.000
22:29569226:A:G	W112R	1.000
22:29569226:A:T	W112R	1.000
22:29558881:A:T	V260D	0.999
22:29558893:C:G	W256S	0.999
22:29558907:C:A	W251C	0.999
22:29558907:C:G	W251C	0.999
22:29558932:C:G	R243P	0.999
22:29558933:G:C	R243G	0.999
22:29560735:C:A	W235C	0.999
22:29560735:C:G	W235C	0.999
22:29560739:A:G	L234P	0.999
22:29560743:G:C	H233D	0.999
22:29560763:C:A	G226V	0.999
22:29560763:C:T	G226E	0.999

dbSNP variants (sampled 300 via entrez): RS1000062643 (22:29579088 T>C), RS1000093507 (22:29578737 C>G), RS1000239687 (22:29558220 A>G), RS1000335266 (22:29572272 C>A,T), RS1000371435 (22:29577145 G>A,C), RS1000468348 (22:29565046 C>A), RS1000590172 (22:29558446 G>A,C), RS1000616784 (22:29558105 CA>C), RS1000858580 (22:29582597 G>A,C), RS1001071836 (22:29557756 C>T), RS1001101513 (22:29576882 G>A), RS1001119982 (22:29577322 G>A,T), RS1001363135 (22:29569985 A>C,G), RS1001571883 (22:29569747 C>T), RS1001584491 (22:29576646 C>T)

Disease associations

OMIM: gene MIM:603249 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST90000025_705	Appendicular lean mass	6.000000e-11

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004980	appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4295933 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
6.07	Kd	856.6	nM	CHEMBL5653589
6.07	ED50	856.6	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 4 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2148868: Binding affinity to human NIPSNAP1 incubated for 45 mins by Kinobead based pull down assay	kd	0.8566	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases methylation, affects cotreatment, decreases expression, affects expression	7
trichostatin A	affects cotreatment, decreases expression	3
bisphenol A	affects expression, increases expression	2
sodium arsenite	decreases expression, increases abundance	2
cobaltous chloride	decreases expression	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression, decreases expression	2
Decitabine	affects expression, increases expression	2
Acetaminophen	decreases expression	2
Arsenic	increases methylation, decreases expression, increases abundance	2
Benzo(a)pyrene	affects methylation, decreases expression	2
Tretinoin	decreases expression, increases expression	2
Cyclosporine	decreases expression	2
aristolochic acid I	decreases expression	1
GSK-J4	decreases expression	1
tetrahydropalmatine	increases expression	1
arsenite	increases reaction, affects binding	1
perfluorooctanoic acid	increases expression	1
periodate-oxidized adenosine	affects expression	1
cupric chloride	decreases expression	1
tamibarotene	increases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
K 7174	decreases expression	1
bisphenol B	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	increases expression, affects cotreatment	1
LDN 193189	affects cotreatment, increases expression	1
NSC 689534	affects binding, decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Bortezomib	decreases expression	1

ChEMBL screening assays

3 unique, capped per target: 3 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL4118594	Binding	Binding affinity to NIPSNAP1 in human NCI-H23 cells at 1 uM by mass spectrometry based pull down assay	Studies of TAK1-centered polypharmacology with novel covalent TAK1 inhibitors. — Bioorg Med Chem

Clinical trials (associated diseases)

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