NIPSNAP3A

Summary

NIPSNAP3A (nipsnap homolog 3A, HGNC:23619) is a protein-coding gene on chromosome 9q31.1, encoding Protein NipSnap homolog 3A (Q9UFN0).

NIPSNAP3A belongs to a family of proteins with putative roles in vesicular transport (Buechler et al., 2004 [PubMed 15177564]).

Source: NCBI Gene 25934 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 47 total
• Druggable target: yes
• MANE Select transcript: NM_015469

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23619
Approved symbol	NIPSNAP3A
Name	nipsnap homolog 3A
Location	9q31.1
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp564D177, FLJ13953, HSPC299, MGC14553, NIPSNAP4, TassC
Ensembl gene	ENSG00000136783
Ensembl biotype	protein_coding
OMIM	608871
Entrez	25934

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000374767, ENST00000471001, ENST00000887912, ENST00000887913, ENST00000887914, ENST00000939849

RefSeq mRNA: 2 — MANE Select: NM_015469 NM_001329570, NM_015469

CCDS: CCDS6760

Canonical transcript exons

ENST00000374767 — 6 exons

Exon	Start	End
ENSE00000805861	104750956	104751166
ENSE00000805865	104754551	104754700
ENSE00001089441	104759262	104760120
ENSE00001464584	104747683	104747852
ENSE00001678294	104759085	104759171
ENSE00001716679	104752906	104753064

Expression profiles

Bgee: expression breadth ubiquitous, 253 present calls, max score 97.72.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 30.2327 / max 354.5567, expressed in 1820 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
97784	16.6374	1809
97783	13.4290	1796
97785	0.1663	65

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adrenal tissue	UBERON:0018303	97.72	gold quality
monocyte	CL:0000576	94.66	gold quality
rectum	UBERON:0001052	94.56	gold quality
palpebral conjunctiva	UBERON:0001812	94.36	gold quality
leukocyte	CL:0000738	94.22	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	94.22	gold quality
spinal cord	UBERON:0002240	94.00	gold quality
right adrenal gland cortex	UBERON:0035827	93.42	gold quality
ileal mucosa	UBERON:0000331	93.07	gold quality
right adrenal gland	UBERON:0001233	93.05	gold quality
left adrenal gland	UBERON:0001234	92.76	gold quality
cortical plate	UBERON:0005343	92.73	gold quality
ganglionic eminence	UBERON:0004023	92.58	gold quality
popliteal artery	UBERON:0002250	92.40	gold quality
tibial artery	UBERON:0007610	92.40	gold quality
adrenal gland	UBERON:0002369	92.29	gold quality
left adrenal gland cortex	UBERON:0035825	92.19	gold quality
right coronary artery	UBERON:0001625	92.04	gold quality
oocyte	CL:0000023	91.91	gold quality
smooth muscle tissue	UBERON:0001135	91.90	gold quality
left coronary artery	UBERON:0001626	91.83	gold quality
adrenal cortex	UBERON:0001235	91.68	gold quality
aorta	UBERON:0000947	91.67	gold quality
descending thoracic aorta	UBERON:0002345	91.31	gold quality
coronary artery	UBERON:0001621	91.08	gold quality
substantia nigra pars compacta	UBERON:0001965	91.02	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.94	gold quality
mucosa of transverse colon	UBERON:0004991	90.85	gold quality
thoracic aorta	UBERON:0001515	90.78	gold quality
ascending aorta	UBERON:0001496	90.70	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-9067	yes	20.69
E-CURD-112	yes	8.56
E-ANND-3	yes	8.10

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

48 targeting NIPSNAP3A, 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-340-5P	100.00	72.50	4437
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-498-3P	99.91	71.27	1114
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-10395-5P	99.86	67.35	676
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-205-5P	99.81	70.05	1557
HSA-MIR-5002-5P	99.76	70.84	1763
HSA-MIR-4766-5P	99.75	69.23	2662
HSA-MIR-587	99.64	70.86	2611
HSA-MIR-569	99.42	66.32	1009
HSA-MIR-889-3P	99.40	69.76	2103
HSA-MIR-1244	99.33	68.38	832
HSA-MIR-4777-5P	99.33	67.53	1148
HSA-MIR-5190	99.15	67.76	1234
HSA-MIR-4795-5P	99.11	66.90	876
HSA-MIR-4504	99.10	69.14	1328

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	nipsnap3a	ENSDARG00000020387
mus_musculus	Nipsnap3a	ENSMUSG00000015242
mus_musculus	Nipsnap3b	ENSMUSG00000015247
rattus_norvegicus	Nipsnap3a	ENSRNOG00000010332
rattus_norvegicus	Nipsnap3a	ENSRNOG00000086685
drosophila_melanogaster	Nipsnap	FBGN0030724
caenorhabditis_elegans		WBGENE00019301

Paralogs (3): NIPSNAP2 (ENSG00000146729), NIPSNAP3B (ENSG00000165028), NIPSNAP1 (ENSG00000184117)

Protein

Protein identifiers

Protein NipSnap homolog 3A — Q9UFN0 (reviewed: Q9UFN0)

Alternative names: Protein NipSnap homolog 4, Target for Salmonella secreted protein C

All UniProt accessions (1): Q9UFN0

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Interacts with the Salmonella typhimurium virulence protein spiC.

Subcellular location. Cytoplasm. Cytosol.

Tissue specificity. Ubiquitous. Highly expressed in liver, kidney and muscle. Expressed at intermediate level in brain, heart, colon, thymus, kidney, small intestine, placenta, lung, leukocytes and spleen.

Similarity. Belongs to the NipSnap family.

RefSeq proteins (2): NP_001316499, NP_056284* (*=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 (6 total): modified residue 2, sequence conflict 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UFN0-F1	91.00	0.86

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): 48, 166

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 85 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_MACROAUTOPHAGY, MCBRYAN_PUBERTAL_BREAST_4_5WK_DN, MCBRYAN_PUBERTAL_BREAST_5_6WK_UP, TANAKA_METHYLATED_IN_ESOPHAGEAL_CARCINOMA, IVANOVA_HEMATOPOIESIS_INTERMEDIATE_PROGENITOR, LEE_RECENT_THYMIC_EMIGRANT, WANG_SMARCE1_TARGETS_UP, GSE13887_HEALTHY_VS_LUPUS_RESTING_CD4_TCELL_UP, GSE13762_CTRL_VS_125_VITAMIND_DAY5_DC_UP, CHICAS_RB1_TARGETS_CONFLUENT, GOBP_AUTOPHAGY_OF_MITOCHONDRION, GOBP_MITOPHAGY, GOBP_PROCESS_UTILIZING_AUTOPHAGIC_MECHANISM

GO Biological Process (1): mitophagy (GO:0000423)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), mitochondrion (GO:0005739), cytosol (GO:0005829), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membrane-bounded organelle	2
cytoplasm	2
cellular anatomical structure	2
autophagy of mitochondrion	1
macroautophagy	1
binding	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

618 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NIPSNAP3A	SPIC	Q8N5J4	934
NIPSNAP3A	ABCA1	O95477	707
NIPSNAP3A	OR13C2	Q8NGS9	582
NIPSNAP3A	OR13D1	Q8NGV5	571
NIPSNAP3A	OR13C9	Q8NGT0	567
NIPSNAP3A	LAMP1	P11279	549
NIPSNAP3A	OR13C5	Q8NGS8	470
NIPSNAP3A	OR13C8	Q8NGS7	414
NIPSNAP3A	HOOK3	Q86VS8	395
NIPSNAP3A	C1orf122	Q6ZSJ8	392
NIPSNAP3A	SLC25A44	Q96H78	380
NIPSNAP3A	MCFD2	Q8NI22	349
NIPSNAP3A	SCAMP4	Q969E2	337
NIPSNAP3A	OPTC	Q9UBM4	329
NIPSNAP3A	ERI3	O43414	326

IntAct

49 interactions, top by confidence:

A	B	Type	Score
HSPD1	NUDT19	psi-mi:“MI:0914”(association)	0.710
CEP70	NIPSNAP3A	psi-mi:“MI:0915”(physical association)	0.560
UBR4	UBE2A	psi-mi:“MI:0914”(association)	0.550
OTC	RTL8C	psi-mi:“MI:0914”(association)	0.530
GATC	NME4	psi-mi:“MI:0914”(association)	0.530
KCMF1	IDH2	psi-mi:“MI:0914”(association)	0.530
NIPSNAP3A	CLUH	psi-mi:“MI:0914”(association)	0.530
FGF13	MARK3	psi-mi:“MI:0914”(association)	0.530
NIPSNAP3A	TP63	psi-mi:“MI:0915”(physical association)	0.510
MAB21L4	NIPSNAP3A	psi-mi:“MI:0915”(physical association)	0.400
	TK2	psi-mi:“MI:0915”(physical association)	0.400
FAM219A	NIPSNAP3A	psi-mi:“MI:0915”(physical association)	0.370
NIPSNAP3A	CCDC90B	psi-mi:“MI:0915”(physical association)	0.370
KIFAP3	NIPSNAP3A	psi-mi:“MI:0915”(physical association)	0.370
ACAD9	A2ML1	psi-mi:“MI:0914”(association)	0.350
NIT1	NUDT19	psi-mi:“MI:0914”(association)	0.350
MRPL12		psi-mi:“MI:0914”(association)	0.350
ATP5F1D		psi-mi:“MI:0914”(association)	0.350
FGL1	DNM1L	psi-mi:“MI:0914”(association)	0.350
SDHB	CLPX	psi-mi:“MI:0914”(association)	0.350
HSDL2	HERC2	psi-mi:“MI:0914”(association)	0.350
PPA2	H1-3	psi-mi:“MI:0914”(association)	0.350
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350

BioGRID (110): CEP70 (Two-hybrid), NIPSNAP3A (Affinity Capture-MS), NIPSNAP3A (Affinity Capture-MS), NIPSNAP3A (Affinity Capture-MS), NIPSNAP3A (Affinity Capture-MS), NIPSNAP3A (Affinity Capture-MS), NIPSNAP3A (Affinity Capture-MS), NIPSNAP3A (Affinity Capture-MS), NIPSNAP3A (Affinity Capture-MS), NIPSNAP3A (Affinity Capture-MS), NIPSNAP3A (Affinity Capture-MS), NIPSNAP3A (Affinity Capture-MS), NIPSNAP3A (Affinity Capture-MS), NIPSNAP3A (Affinity Capture-MS), NIPSNAP3A (Affinity Capture-MS)

ESM2 similar proteins: A0A063C1W0, A0A2I1C3W7, A0A411PQP6, A0A4P8DJD9, A0A5B8YU67, A0AKL8, B3MR30, B3P9N0, B4I9J6, B4M7S0, B4PY69, B4R313, B9DKR5, C1KX66, E1ACR2, F4I1L3, F6NVH9, I1RVD6, O46084, O55125, O55126, O75323, P0CU76, P34492, P91929, Q09422, Q12931, Q19000, Q29HG0, Q2TBI4, Q4WQY7, Q502L2, Q54I58, Q562B5, Q5FWM4, Q5RAA9, Q61CA3, Q6GL33, Q71XQ0, Q8BX10

Diamond homologs: Q5RAA9, Q9BS92, Q9CQE1, Q9UFN0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 50 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
Mitochondrial protein degradation	5	16.3×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	34
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

979 predictions. Top by Δscore:

Variant	Effect	Δscore
9:104747849:TCAGG:T	donor_loss	1.0000
9:104747851:AG:A	donor_loss	1.0000
9:104747852:GGTAC:G	donor_loss	1.0000
9:104747853:GT:G	donor_loss	1.0000
9:104747854:T:G	donor_loss	1.0000
9:104750950:CTTCA:C	acceptor_loss	1.0000
9:104750952:TCAG:T	acceptor_loss	1.0000
9:104750953:CAG:C	acceptor_loss	1.0000
9:104750955:G:GC	acceptor_loss	1.0000
9:104750955:GAT:G	acceptor_gain	1.0000
9:104750955:GATGT:G	acceptor_gain	1.0000
9:104751128:G:GT	donor_gain	1.0000
9:104751159:G:GT	donor_gain	1.0000
9:104751159:G:T	donor_gain	1.0000
9:104751162:GTATG:G	donor_gain	1.0000
9:104751195:G:GG	donor_gain	1.0000
9:104752902:ACAG:A	acceptor_loss	1.0000
9:104752903:C:G	acceptor_gain	1.0000
9:104752903:CAGA:C	acceptor_loss	1.0000
9:104752904:A:AG	acceptor_gain	1.0000
9:104752904:AGAT:A	acceptor_loss	1.0000
9:104752905:G:GG	acceptor_gain	1.0000
9:104752905:GA:G	acceptor_gain	1.0000
9:104752905:GAT:G	acceptor_gain	1.0000
9:104752905:GATA:G	acceptor_gain	1.0000
9:104752905:GATAA:G	acceptor_gain	1.0000
9:104753060:AGAAG:A	donor_gain	1.0000
9:104753061:GAAG:G	donor_gain	1.0000
9:104753061:GAAGG:G	donor_gain	1.0000
9:104753062:AAG:A	donor_gain	1.0000

AlphaMissense

1607 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:104751112:T:A	W73R	0.972
9:104751112:T:C	W73R	0.972
9:104752921:G:C	R96P	0.963
9:104754670:T:C	F184L	0.963
9:104754672:C:A	F184L	0.963
9:104754672:C:G	F184L	0.963
9:104754601:T:A	W161R	0.962
9:104754601:T:C	W161R	0.962
9:104759270:A:C	S226R	0.961
9:104759272:T:A	S226R	0.961
9:104759272:T:G	S226R	0.961
9:104754665:G:A	G182E	0.947
9:104751107:G:A	G71E	0.945
9:104753034:T:A	W134R	0.945
9:104753034:T:C	W134R	0.945
9:104759121:G:C	R206P	0.944
9:104754696:C:A	N192K	0.943
9:104754696:C:G	N192K	0.943
9:104754563:T:C	L148P	0.942
9:104754571:T:C	F151L	0.940
9:104754573:T:A	F151L	0.940
9:104754573:T:G	F151L	0.940
9:104759085:T:A	V194D	0.939
9:104751157:T:A	W88R	0.934
9:104751157:T:C	W88R	0.934
9:104759307:T:C	L238P	0.931
9:104754556:T:G	Y146D	0.929
9:104759134:A:C	R210S	0.926
9:104759134:A:T	R210S	0.926
9:104759120:C:A	R206S	0.924

dbSNP variants (sampled 300 via entrez): RS1000038817 (9:104756151 G>A), RS1000130806 (9:104756993 A>G), RS1000170407 (9:104752219 TAAA>T), RS1000226865 (9:104751865 A>G), RS1000638128 (9:104754947 T>C), RS1000711798 (9:104758345 A>G), RS1000762209 (9:104758803 T>A,C), RS1001135433 (9:104754683 A>T), RS1001179001 (9:104753946 A>G), RS1001304344 (9:104747893 G>A,C), RS1001718817 (9:104760166 G>C), RS1001814721 (9:104748508 A>G), RS1001896882 (9:104754070 T>C), RS1002108521 (9:104760343 T>C), RS1002239351 (9:104755209 C>G)

Disease associations

OMIM: gene MIM:608871 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST001904_4	HDL cholesterol	6.000000e-26
GCST002343_6	Response to cytidine analogues (gemcitabine)	4.000000e-06
GCST007446_53	vWF levels	2.000000e-08
GCST008163_74	Height	6.000000e-06
GCST009391_736	Metabolite levels	2.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004612	high density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3817722 (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
5.66	Kd	2177	nM	CHEMBL5653589
5.66	ED50	2177	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 5 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	2148869: Binding affinity to human NIPSNAP3A incubated for 45 mins by Kinobead based pull down assay	kd	2.1767	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
methylmercuric chloride	decreases expression	3
sodium arsenite	decreases expression	2
Air Pollutants	decreases expression, increases abundance	2
Rotenone	increases expression	2
Smoke	decreases expression, increases abundance	2
Aflatoxin B1	decreases expression, decreases methylation	2
aristolochic acid I	increases expression	1
dicrotophos	decreases expression	1
sodium arsenate	decreases expression	1
methylparaben	decreases expression	1
sulforaphane	decreases expression	1
cobaltous chloride	decreases expression	1
perfluorooctanoic acid	increases expression	1
perfluorooctane sulfonic acid	decreases expression	1
azoxystrobin	increases expression	1
abrine	decreases expression	1
bisphenol AF	increases expression	1
Acetaminophen	decreases expression	1
Cisplatin	increases expression	1
Coal	decreases expression, increases abundance	1
Hydrogen Peroxide	affects expression	1
Ivermectin	decreases expression	1
Phenobarbital	affects expression	1
Quercetin	decreases expression	1
Tetrachlorodibenzodioxin	decreases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	affects expression	1
Urethane	decreases expression	1
Valproic Acid	decreases expression	1
Cadmium Chloride	increases expression	1

ChEMBL screening assays

2 unique, capped per target: 1 admet, 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL3821396	ADMET	Binding affinity to NIPSNAP3A in human HepG2 assessed as intensity fold change of cumulated normalized intensity of protein between capture and competition assay at 100 uM after 1 hr in presence of inactive Tcp-CC 14 by differential competi	Identification of Potential Off-target Toxicity Liabilities of Catechol-O-methyltransferase Inhibitors by Differential Competition Capture Compound Mass Spectrometry. — J Med Chem
CHEMBL5651911	Binding	Binding affinity to human NIPSNAP3A incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_TA74	HAP1 NIPSNAP3A (-) 1	Cancer cell line	Male
CVCL_XQ96	HAP1 NIPSNAP3A (-) 2	Cancer cell line	Male
CVCL_XQ97	HAP1 NIPSNAP3A (-) 3	Cancer cell line	Male
CVCL_XQ98	HAP1 NIPSNAP3A (-) 4	Cancer cell line	Male

Clinical trials (associated diseases)

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