NPIPB3

Summary

NPIPB3 (nuclear pore complex interacting protein family member B3, HGNC:28989) is a protein-coding gene on chromosome 16p12.2, encoding Nuclear pore complex-interacting protein family member B3 (Q92617).

Predicted to be located in nuclear envelope.

Source: NCBI Gene 23117 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 15 total

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28989
Approved symbol	NPIPB3
Name	nuclear pore complex interacting protein family member B3
Location	16p12.2
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0220
Ensembl gene	ENSG00000169246
Ensembl biotype	protein_coding
OMIM	619984
Entrez	23117

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 6 protein_coding_CDS_not_defined, 5 protein_coding, 2 retained_intron

ENST00000419180, ENST00000504841, ENST00000519305, ENST00000521589, ENST00000534903, ENST00000535190, ENST00000537983, ENST00000538439, ENST00000542817, ENST00000542953, ENST00000543368, ENST00000544154, ENST00000545358

RefSeq mRNA: 1 — MANE Select: None NM_130464

Canonical transcript exons

ENST00000419180 — 9 exons

Exon	Start	End
ENSE00001713363	21406654	21406689
ENSE00002208119	21425300	21425322
ENSE00002300087	21405173	21405293
ENSE00003460386	21414957	21415085
ENSE00003518762	21410934	21411129
ENSE00003535140	21406799	21406859
ENSE00003561690	21424979	21425136
ENSE00003569032	21419490	21419575
ENSE00003635358	21411242	21411341

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 99.44.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	99.44	gold quality
right hemisphere of cerebellum	UBERON:0014890	99.33	gold quality
cerebellar hemisphere	UBERON:0002245	99.24	gold quality
cerebellar cortex	UBERON:0002129	99.22	gold quality
cerebellum	UBERON:0002037	99.16	gold quality
spleen	UBERON:0002106	99.16	gold quality
granulocyte	CL:0000094	99.14	gold quality
endocervix	UBERON:0000458	99.12	gold quality
left lobe of thyroid gland	UBERON:0001120	99.12	gold quality
mucosa of stomach	UBERON:0001199	99.10	gold quality
pituitary gland	UBERON:0000007	99.08	gold quality
skin of abdomen	UBERON:0001416	99.08	gold quality
zone of skin	UBERON:0000014	99.06	gold quality
small intestine Peyer’s patch	UBERON:0003454	99.06	gold quality
skin of leg	UBERON:0001511	99.05	gold quality
adenohypophysis	UBERON:0002196	99.01	gold quality
lower esophagus mucosa	UBERON:0035834	99.00	gold quality
right lobe of thyroid gland	UBERON:0001119	98.96	gold quality
right frontal lobe	UBERON:0002810	98.91	gold quality
muscle layer of sigmoid colon	UBERON:0035805	98.91	gold quality
left uterine tube	UBERON:0001303	98.84	gold quality
right ovary	UBERON:0002118	98.84	gold quality
subcutaneous adipose tissue	UBERON:0002190	98.84	gold quality
metanephros cortex	UBERON:0010533	98.83	gold quality
transverse colon	UBERON:0001157	98.82	gold quality
thyroid gland	UBERON:0002046	98.82	gold quality
sural nerve	UBERON:0015488	98.82	gold quality
tibial nerve	UBERON:0001323	98.79	gold quality
uterine cervix	UBERON:0000002	98.77	gold quality
ectocervix	UBERON:0012249	98.75	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-GEOD-130473	yes	946.19
E-MTAB-7052	yes	148.58
E-ANND-3	yes	6.05
E-MTAB-6678	yes	5.50
E-MTAB-7381	no	799.85

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting NPIPB3, 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-656-3P	100.00	72.15	2788
HSA-MIR-6759-5P	99.99	66.54	785
HSA-MIR-6793-5P	99.97	65.95	758
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-3934-3P	99.76	65.51	1351
HSA-MIR-17-3P	99.55	66.77	1311
HSA-MIR-6739-3P	99.22	68.84	1843
HSA-MIR-16-1-3P	98.70	69.23	1538
HSA-MIR-122-5P	97.23	64.92	1024
HSA-MIR-1288-3P	96.86	66.95	536
HSA-MIR-3169	96.40	67.58	698

Literature-anchored findings (GeneRIF, showing 1)

• The overexpression of NPIPB3 restored the interferon-beta responses in severe acute respiratory syndrome coronavirus open reading frame 6 (SARS-CoV ORF6) expressing cells, indicating that the interaction of SARS CoV ORF6 and NPIPB3 reduced Type I interferon antagonism by SARS-CoV ORF6. (PMID:26320399)

Cross-species orthologs

0 orthologs

Paralogs (19): NPIPB12 (ENSG00000169203), NPIPA1 (ENSG00000183426), NPIPA5 (ENSG00000183793), NPIPA6 (ENSG00000183889), NPIPB4 (ENSG00000185864), NPIPB15 (ENSG00000196436), NPIPB9 (ENSG00000196993), NPIPB13 (ENSG00000198064), NPIPB6 (ENSG00000198156), NPIPA8 (ENSG00000214940), NPIPA7 (ENSG00000214967), NPIPA3 (ENSG00000224712), NPIPA9 (ENSG00000233024), NPIPB7 (ENSG00000233232), NPIPB2 (ENSG00000234719), NPIPB5 (ENSG00000243716), NPIPB11 (ENSG00000254206), NPIPA2 (ENSG00000254852), NPIPB8 (ENSG00000255524)

Protein

Protein identifiers

Nuclear pore complex-interacting protein family member B3 — Q92617 (reviewed: Q92617)

Alternative names: Nuclear pore complex-interacting protein-like 3, Protein pps22-1

All UniProt accessions (5): Q92617, C9K082, E9PR77, F5H3W2, F5H4N5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the NPIP family.

Isoforms (6)

UniProt ID	Names	Canonical?
Q92617-1	1	yes
Q92617-2	2
Q92617-3	3
Q92617-4	4
Q92617-5	5
Q92617-6	6

RefSeq proteins (1): NP_569731 (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009443	NPIP	Family
IPR048893	NPB13-like_MII_rpt	Repeat
IPR054697	NPIP_N	Domain

Pfam: PF06409, PF20885

UniProt features (38 total): sequence conflict 15, compositionally biased region 9, splice variant 9, region of interest 3, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q92617-F1	44.45	0.00

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-9692916	SARS-CoV-1 activates/modulates innate immune responses

MSigDB gene sets: 66 (showing top): MODULE_169, PEREZ_TP63_TARGETS, ASTON_MAJOR_DEPRESSIVE_DISORDER_DN, HSIAO_HOUSEKEEPING_GENES, BROWNE_HCMV_INFECTION_12HR_UP, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5, BROWNE_HCMV_INFECTION_48HR_DN, ONKEN_UVEAL_MELANOMA_UP, SMID_BREAST_CANCER_LUMINAL_B_UP, PEREZ_TP53_AND_TP63_TARGETS, HAHTOLA_SEZARY_SYNDROM_UP, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP, HOEBEKE_LYMPHOID_STEM_CELL_UP, CHANDRAN_METASTASIS_UP, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN

GO Biological Process (0):

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

GO Cellular Component (2): nuclear envelope (GO:0005635), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
SARS-CoV-1-host interactions	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
nucleus	1
endomembrane system	1
organelle envelope	1
cellular anatomical structure	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

6 interactions, top by confidence:

A	B	Type	Score
	NPIPB3	psi-mi:“MI:0915”(physical association)	0.570
	NPIPB3	psi-mi:“MI:0407”(direct interaction)	0.570
NPIPB3		psi-mi:“MI:0403”(colocalization)	0.570
recC	NPIPB3	psi-mi:“MI:0915”(physical association)	0.000
NPIPB3		psi-mi:“MI:0915”(physical association)	0.000

BioGRID (7): NPIPB3 (Affinity Capture-MS), NPIPB3 (Biochemical Activity), NPIPB3 (Affinity Capture-RNA), NPIPB3 (Negative Genetic), NPIPB3 (Protein-peptide), ORF6 (Affinity Capture-Western), NPIPB3 (Affinity Capture-RNA)

ESM2 similar proteins: A0A023PXQ4, A0A0U1RQI7, A6NJU9, A6NNC1, A8MRT5, A8MUU9, C9JG80, E2RYF6, E5RHQ5, F8W0I5, O13534, O59779, P08399, P0C732, P0C785, P0DTH6, P0DW28, P13208, P15941, P21787, P24856, P39564, P51861, P87269, Q00130, Q01456, Q12444, Q13117, Q1HVI8, Q27905, Q2EEQ3, Q4ZJY7, Q4ZJZ0, Q5SDL7, Q63661, Q69577, Q6B0Y1, Q6RY98, Q6ZQT0, Q6ZRX8

Diamond homologs: A0A0B4J1W7, A6NHN6, A6NJ64, A6NJU9, A8MRT5, C9JG80, E5RHQ5, E9PIF3, E9PJ23, E9PJI5, E9PKD4, E9PQR5, F8W0I5, F8W1W9, F8WFD2, O75200, P0DM63, P0DXC3, Q92617, Q9UND3, O70490, Q08AH1, Q08AH3, Q3UNX5, Q53FZ2, Q5REV5, Q68CK6, Q6AYT9, Q6NUN0, Q6SKG1, Q8BGA8, Q8K0L3, Q91VA0, Q9BEA2, A0A179HJB8, A4YDT1, C0SPB0, P0C7M7, P39062, Q6P461

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	9
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

1631 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1004194121 (16:21410669 A>G), RS1008753376 (16:21401840 A>AAGTT), RS1009447408 (16:21401805 G>A), RS1015786374 (16:21412218 A>G), RS1019690554 (16:21401843 T>G), RS1027085496 (16:21409621 C>T), RS1027438144 (16:21402064 A>G), RS1034224118 (16:21416712 C>G), RS1039310550 (16:21409587 C>G), RS1042304363 (16:21409099 A>G), RS1042336349 (16:21401821 G>C), RS1050212105 (16:21416976 C>T), RS1053897483 (16:21401753 T>TAAAC), RS1061048 (16:21425151 A>T), RS112190881 (16:21401987 G>A,C)

Disease associations

OMIM: gene MIM:619984 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Cadmium	decreases expression, increases abundance	2
Particulate Matter	increases expression, affects cotreatment, increases abundance	2
bisphenol F	affects cotreatment, decreases expression	1
dicrotophos	increases expression	1
bisphenol A	increases expression	1
2,5,2’,5’-tetrachlorobiphenyl	decreases expression	1
manganese chloride	decreases expression, increases abundance	1
tamibarotene	affects expression	1
bisphenol S	affects cotreatment, decreases expression	1
Cocaine	increases expression	1
Demecolcine	increases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Heroin	increases expression	1
Estradiol	increases expression	1
Gasoline	affects cotreatment, increases abundance, increases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Malathion	decreases expression	1
Manganese	decreases expression, increases abundance	1
Polycyclic Aromatic Hydrocarbons	increases abundance, increases expression, affects cotreatment	1
Dronabinol	increases expression	1
Tretinoin	affects expression	1
Vincristine	decreases expression	1
Vitamin E	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Asbestos, Crocidolite	decreases expression	1
Cadmium Chloride	decreases expression, increases abundance	1
Lactic Acid	increases expression	1
Genistein	increases expression	1
Acrylamide	increases expression	1
Permethrin	decreases expression	1

Clinical trials (associated diseases)

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