NIPSNAP3B

Summary

NIPSNAP3B (nipsnap homolog 3B, HGNC:23641) is a protein-coding gene on chromosome 9q31.1, encoding Protein NipSnap homolog 3B (Q9BS92).

NIPSNAP3B belongs to a family of proteins with putative roles in vesicular trafficking (Buechler et al., 2004 [PubMed 15177564]).

Source: NCBI Gene 55335 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 57 total — 1 pathogenic, 1 likely-pathogenic
• MANE Select transcript: NM_018376

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23641
Approved symbol	NIPSNAP3B
Name	nipsnap homolog 3B
Location	9q31.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ11275, NIPSNAP3, SNAP1
Ensembl gene	ENSG00000165028
Ensembl biotype	protein_coding
OMIM	608872
Entrez	55335

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000374762, ENST00000460936, ENST00000461177, ENST00000900308, ENST00000900309

RefSeq mRNA: 1 — MANE Select: NM_018376 NM_018376

CCDS: CCDS6761

Canonical transcript exons

ENST00000374762 — 6 exons

Exon	Start	End
ENSE00001089450	104766325	104766535
ENSE00001368826	104764129	104764300
ENSE00001385015	104772997	104777764
ENSE00003489072	104768863	104769021
ENSE00003662655	104772822	104772908
ENSE00003668860	104770849	104770998

Expression profiles

Bgee: expression breadth ubiquitous, 210 present calls, max score 94.83.

FANTOM5 (CAGE): breadth broad, TPM avg 3.0082 / max 59.1616, expressed in 901 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
97786	1.5594	613
97787	1.4337	507
97788	0.0150	7

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
biceps brachii	UBERON:0001507	94.83	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	93.24	gold quality
heart right ventricle	UBERON:0002080	92.16	gold quality
hindlimb stylopod muscle	UBERON:0004252	90.80	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	90.26	gold quality
diaphragm	UBERON:0001103	88.94	gold quality
deltoid	UBERON:0001476	88.15	silver quality
skeletal muscle tissue	UBERON:0001134	87.38	gold quality
vastus lateralis	UBERON:0001379	86.74	gold quality
right adrenal gland cortex	UBERON:0035827	86.59	gold quality
muscle organ	UBERON:0001630	86.50	gold quality
muscle of leg	UBERON:0001383	86.29	gold quality
tibialis anterior	UBERON:0001385	86.28	gold quality
gastrocnemius	UBERON:0001388	86.02	gold quality
right adrenal gland	UBERON:0001233	85.94	gold quality
muscle tissue	UBERON:0002385	85.82	gold quality
quadriceps femoris	UBERON:0001377	85.77	gold quality
left ventricle myocardium	UBERON:0006566	85.65	gold quality
heart left ventricle	UBERON:0002084	85.56	gold quality
cardiac ventricle	UBERON:0002082	85.48	gold quality
left adrenal gland	UBERON:0001234	85.42	gold quality
left adrenal gland cortex	UBERON:0035825	85.22	gold quality
adrenal tissue	UBERON:0018303	85.06	gold quality
adrenal cortex	UBERON:0001235	83.77	gold quality
heart	UBERON:0000948	83.73	gold quality
adrenal gland	UBERON:0002369	83.69	gold quality
myocardium	UBERON:0002349	83.18	gold quality
adipose tissue	UBERON:0001013	82.67	gold quality
right atrium auricular region	UBERON:0006631	81.90	gold quality
adipose tissue of abdominal region	UBERON:0007808	81.87	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.48

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

161 targeting NIPSNAP3B, 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-4668-3P	100.00	68.74	2635
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-4715-3P	99.98	66.03	670
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3605-5P	99.96	67.12	932
HSA-MIR-590-3P	99.96	74.34	6478
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-651-3P	99.94	73.48	5177
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-3682-5P	99.93	67.97	1163
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-498-3P	99.91	71.27	1114
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394

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): NIPSNAP3A (ENSG00000136783), NIPSNAP2 (ENSG00000146729), NIPSNAP1 (ENSG00000184117)

Protein

Protein identifiers

Protein NipSnap homolog 3B — Q9BS92 (reviewed: Q9BS92)

Alternative names: SNAP1

All UniProt accessions (2): Q9BS92, F2Z3L7

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the NipSnap family.

RefSeq proteins (1): NP_060846* (*=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 (7 total): sequence variant 3, modified residue 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BS92-F1	91.54	0.84

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): 45, 57

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 86 (showing top): XU_HGF_TARGETS_REPRESSED_BY_AKT1_DN, GOBP_MACROAUTOPHAGY, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, TANAKA_METHYLATED_IN_ESOPHAGEAL_CARCINOMA, LAIHO_COLORECTAL_CANCER_SERRATED_DN, GSE13762_CTRL_VS_125_VITAMIND_DAY12_DC_UP, DODD_NASOPHARYNGEAL_CARCINOMA_DN, TST1_01, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_DN, GOBP_AUTOPHAGY_OF_MITOCHONDRION, GOBP_MITOPHAGY, GOBP_PROCESS_UTILIZING_AUTOPHAGIC_MECHANISM, GSE14415_ACT_VS_CTRL_NATURAL_TREG_UP, ZNF257_TARGET_GENES, ZNF282_TARGET_GENES

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

GO Molecular Function (0):

GO Cellular Component (1): mitochondrion (GO:0005739)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
autophagy of mitochondrion	1
macroautophagy	1
cytoplasm	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

444 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NIPSNAP3B	SPIC	Q8N5J4	840
NIPSNAP3B	ABCA1	O95477	715
NIPSNAP3B	LAMP1	P11279	548
NIPSNAP3B	ITK	Q08881	525
NIPSNAP3B	SUSD1	Q6UWL2	494
NIPSNAP3B	SLC46A2	Q9BY10	433
NIPSNAP3B	TDRD3	Q9H7E2	405
NIPSNAP3B	SMIM11	P58511	354
NIPSNAP3B	ASB12	Q8WXK4	342
NIPSNAP3B	HHATL	Q9HCP6	330
NIPSNAP3B	OPTC	Q9UBM4	320
NIPSNAP3B	FKTN	O75072	317
NIPSNAP3B	FSD1L	Q9BXM9	311
NIPSNAP3B	ZNF483	Q8TF39	303
NIPSNAP3B	PKDREJ	Q9NTG1	297
NIPSNAP3B	SWT1	Q5T5J6	297

IntAct

6 interactions, top by confidence:

A	B	Type	Score
NIPSNAP3A	CLUH	psi-mi:“MI:0914”(association)	0.530
NIPSNAP3B	GLS	psi-mi:“MI:0914”(association)	0.350
NIPSNAP3B	CLUH	psi-mi:“MI:0914”(association)	0.350

BioGRID (21): NIPSNAP3B (Co-fractionation), PDK1 (Affinity Capture-MS), PDK2 (Affinity Capture-MS), GLS (Affinity Capture-MS), NIPSNAP3B (Affinity Capture-MS), DBT (Affinity Capture-MS), MTIF2 (Affinity Capture-MS), PDK3 (Affinity Capture-MS), HSPD1 (Affinity Capture-MS), CPS1 (Affinity Capture-MS), LACTB (Affinity Capture-MS), CLUH (Affinity Capture-MS), TARS2 (Affinity Capture-MS), ACSF2 (Affinity Capture-MS), PRPS1L1 (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: Q5RAA9, Q9BS92, Q9CQE1, Q9UFN0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	1
Uncertain significance	38
Likely benign	5
Benign	4

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
9502	NM_005502.4(ABCA1):c.6026T>C (p.Phe2009Ser)	Pathogenic
9494	NM_005502.4(ABCA1):c.6241C>T (p.Arg2081Trp)	Likely pathogenic

SpliceAI

967 predictions. Top by Δscore:

Variant	Effect	Δscore
9:104764299:AGGT:A	donor_loss	1.0000
9:104764301:G:GA	donor_loss	1.0000
9:104764302:T:A	donor_loss	1.0000
9:104766324:GGTGT:G	acceptor_gain	1.0000
9:104766528:G:GT	donor_gain	1.0000
9:104766528:G:T	donor_gain	1.0000
9:104766531:GTATG:G	donor_gain	1.0000
9:104766564:G:GG	donor_gain	1.0000
9:104768858:CATA:C	acceptor_loss	1.0000
9:104768859:ATAG:A	acceptor_loss	1.0000
9:104768860:T:G	acceptor_gain	1.0000
9:104768860:TA:T	acceptor_loss	1.0000
9:104768861:A:AG	acceptor_gain	1.0000
9:104768861:A:G	acceptor_loss	1.0000
9:104768862:G:GG	acceptor_gain	1.0000
9:104768862:GA:G	acceptor_gain	1.0000
9:104768862:GAT:G	acceptor_gain	1.0000
9:104768862:GATA:G	acceptor_gain	1.0000
9:104768862:GATAA:G	acceptor_gain	1.0000
9:104769017:AGAAG:A	donor_gain	1.0000
9:104769018:GAAG:G	donor_gain	1.0000
9:104769018:GAAGG:G	donor_gain	1.0000
9:104769019:AAG:A	donor_gain	1.0000
9:104769020:AG:A	donor_gain	1.0000
9:104769021:GG:G	donor_gain	1.0000
9:104769022:G:GA	donor_loss	1.0000
9:104769022:G:GG	donor_gain	1.0000
9:104770844:TCTA:T	acceptor_loss	1.0000
9:104770846:TA:T	acceptor_loss	1.0000
9:104770848:GGA:G	acceptor_gain	1.0000

AlphaMissense

1608 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:104770968:T:C	F184L	0.977
9:104770970:C:A	F184L	0.977
9:104770970:C:G	F184L	0.977
9:104766481:T:A	W73R	0.976
9:104766481:T:C	W73R	0.976
9:104770869:T:C	F151L	0.965
9:104770871:T:A	F151L	0.965
9:104770871:T:G	F151L	0.965
9:104770899:T:A	W161R	0.963
9:104770899:T:C	W161R	0.963
9:104773005:A:C	S226R	0.963
9:104773007:T:A	S226R	0.963
9:104773007:T:G	S226R	0.963
9:104772858:G:C	R206P	0.961
9:104772857:C:A	R206S	0.957
9:104770854:T:G	Y146D	0.955
9:104770963:G:A	G182D	0.952
9:104772871:A:C	R210S	0.951
9:104772871:A:T	R210S	0.951
9:104766476:G:A	G71E	0.948
9:104770861:T:C	L148P	0.948
9:104772822:T:A	V194D	0.948
9:104768878:G:C	R96P	0.947
9:104770969:T:C	F184S	0.944
9:104773000:G:C	R224P	0.940
9:104773042:T:C	L238P	0.940
9:104772833:T:A	W198R	0.939
9:104772833:T:C	W198R	0.939
9:104773027:A:C	Q233P	0.939
9:104772828:T:A	V196D	0.938

dbSNP variants (sampled 300 via entrez): RS1000312606 (9:104789454 G>C), RS1000372090 (9:104775280 C>G), RS1000488212 (9:104774921 C>G), RS1000542936 (9:104770497 A>G), RS1000587123 (9:104764111 A>C), RS1000654458 (9:104764892 C>G,T), RS1000828107 (9:104783220 G>A), RS1000889720 (9:104780381 A>G,T), RS1001113126 (9:104771902 CT>C), RS1001198807 (9:104780903 T>C), RS1001267024 (9:104787967 G>A), RS1001321925 (9:104780108 A>G), RS1001366642 (9:104778324 A>G), RS1001370170 (9:104791250 G>A), RS1001798669 (9:104790856 C>T)

Disease associations

OMIM: gene MIM:608872 | disease phenotypes: MIM:205400, MIM:604091

GenCC curated gene-disease

Mondo (2): Tangier disease (MONDO:0008783), hypoalphalipoproteinemia, primary, 1 (MONDO:0011393)

Orphanet (2): Tangier disease (Orphanet:31150), Apolipoprotein A-I deficiency (Orphanet:425)

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST001762_590	Obesity-related traits	3.000000e-06
GCST001904_4	HDL cholesterol	6.000000e-26
GCST007446_53	vWF levels	2.000000e-08
GCST009391_1795	Metabolite levels	4.000000e-06
GCST009391_759	Metabolite levels	6.000000e-06

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0010449	3-methyladipic acid measurement
EFO:0010524	pimelic acid measurement
EFO:0010391	sphingomyelin 16:0 measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D013631	Tangier Disease	C10.668.829.800.875; C16.320.565.398.500.330.750; C18.452.584.500.875.330.750; C18.452.584.563.500.330.750; C18.452.648.398.500.330.750

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
triphenyl phosphate	affects expression	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
pentanal	decreases expression	1
avobenzone	decreases expression	1
Sunitinib	increases expression	1
Arsenic	affects methylation	1
Asbestos	affects expression	1
Benzo(a)pyrene	affects methylation	1
Cisplatin	decreases expression, increases expression	1
Diethylhexyl Phthalate	decreases expression	1
Estradiol	affects expression	1
Nickel	decreases expression	1
Silicon Dioxide	decreases expression	1
Thimerosal	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	decreases methylation	1
Vanadates	decreases expression	1
Vitamin E	decreases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT01763528	PHASE3	COMPLETED	High Protein Weight Loss Diet, High Sensitivity C-Reactive Protein and Cardiovascular Risks Among Obese Women
NCT01886482	PHASE3	COMPLETED	Effect of High Protein Diet on Cardiovascular Diseases Risk Factors Among Overweight and Obese Children
NCT01886495	PHASE3	COMPLETED	Effect of High Protein Diet on Adiponectin and Inflammation Among Overweight and Obese Children
NCT06533865	PHASE3	RECRUITING	Romosozumab as an Adjunct to Physiologic Estrogen Replacement in Functional Hypothalamic Amenorrhea
NCT00106782	PHASE2	COMPLETED	Transcranial Electrical Polarization to Treat Focal Hand Dystonia
NCT07010146	PHASE2	RECRUITING	Role of Estrogen on Skeletal Outcomes in FHA
NCT00005188	Not specified	COMPLETED	Quantitative Genetic Analysis of Lipid Research Clinic Family Data
NCT01782027	Not specified	TERMINATED	Mendelian Reverse Cholesterol Transport Study
NCT00453219	Not specified	WITHDRAWN	FHA: Characterization of Metabolic Status, Brain Circuitry, and Stress-Reactivity
NCT06571578	Not specified	COMPLETED	High Intensity Interval Inspiratory Training Effect on Ventilatory Functions and Diaphragmatic Excursion in Forward Head Posture