NPIPB2

Summary

NPIPB2 (nuclear pore complex interacting protein family member B2, HGNC:37451) is a protein-coding gene on chromosome 16p13.13, encoding Nuclear pore complex-interacting protein family member B2 (A6NJ64).

Predicted to be located in nucleus.

Source: NCBI Gene 729978 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 22 total
• MANE Select transcript: NM_001396485

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37451
Approved symbol	NPIPB2
Name	nuclear pore complex interacting protein family member B2
Location	16p13.13
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000234719
Ensembl biotype	protein_coding
Entrez	729978

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 5 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000356023, ENST00000399147, ENST00000532936, ENST00000538896, ENST00000540412, ENST00000547494, ENST00000673243, ENST00000698171

RefSeq mRNA: 6 — MANE Select: NM_001396485 NM_001355514, NM_001395852, NM_001395853, NM_001395854, NM_001395855, NM_001396485

CCDS: CCDS92109, CCDS92110

Canonical transcript exons

ENST00000399147 — 8 exons

Exon	Start	End
ENSE00001593002	11927373	11927879
ENSE00001665317	11929240	11929275
ENSE00001716564	11929385	11929445
ENSE00001805085	11930450	11930551
ENSE00002302160	11941983	11942045
ENSE00002303591	11933517	11933712
ENSE00003484419	11933825	11933924
ENSE00003495807	11937540	11937668

Expression profiles

Bgee: expression breadth ubiquitous, 138 present calls, max score 99.69.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.1270 / max 50.1962, expressed in 1291 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
156336	3.1270	1291

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar vermis	UBERON:0004720	99.69	gold quality
thymus	UBERON:0002370	98.47	gold quality
quadriceps femoris	UBERON:0001377	98.39	gold quality
right testis	UBERON:0004534	89.56	gold quality
left testis	UBERON:0004533	89.53	gold quality
testis	UBERON:0000473	88.38	gold quality
mucosa of stomach	UBERON:0001199	85.08	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.87	gold quality
right hemisphere of cerebellum	UBERON:0014890	84.83	gold quality
cortex of kidney	UBERON:0001225	84.72	gold quality
primary visual cortex	UBERON:0002436	84.32	gold quality
cerebellum	UBERON:0002037	84.14	gold quality
cerebellar cortex	UBERON:0002129	84.08	gold quality
cerebellar hemisphere	UBERON:0002245	83.96	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.81	gold quality
right uterine tube	UBERON:0001302	82.93	gold quality
cortical plate	UBERON:0005343	82.86	gold quality
sural nerve	UBERON:0015488	82.83	gold quality
tonsil	UBERON:0002372	82.68	gold quality
superior frontal gyrus	UBERON:0002661	82.68	gold quality
stromal cell of endometrium	CL:0002255	82.48	gold quality
subcutaneous adipose tissue	UBERON:0002190	82.12	gold quality
skin of leg	UBERON:0001511	81.87	gold quality
zone of skin	UBERON:0000014	81.70	gold quality
left ovary	UBERON:0002119	81.56	gold quality
skin of abdomen	UBERON:0001416	81.48	gold quality
metanephros cortex	UBERON:0010533	81.46	gold quality
right lobe of liver	UBERON:0001114	81.26	gold quality
ovary	UBERON:0000992	81.00	gold quality
thoracic mammary gland	UBERON:0005200	80.88	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• sPLA2-X induces potent arachidonic acid release without activation of cytosolic phospholipase A2 alpha. (PMID:15789617)

Cross-species orthologs

0 orthologs

Paralogs (19): NPIPB12 (ENSG00000169203), NPIPB3 (ENSG00000169246), 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), NPIPB5 (ENSG00000243716), NPIPB11 (ENSG00000254206), NPIPA2 (ENSG00000254852), NPIPB8 (ENSG00000255524)

Protein

Protein identifiers

Nuclear pore complex-interacting protein family member B2 — A6NJ64 (reviewed: A6NJ64)

All UniProt accessions (5): A6NJ64, A0A5F9ZI19, A0A8V8TLJ1, F5H898, F8VY45

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

Similarity. Belongs to the NPIP family.

RefSeq proteins (6): NP_001342443, NP_001382781, NP_001382782, NP_001382783, NP_001382784, NP_001383414* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009443	NPIP	Family
IPR054697	NPIP_N	Domain

Pfam: PF06409

UniProt features (5 total): compositionally biased region 3, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NJ64-F1	56.54	0.04

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 9 (showing top): ARNT2_TARGET_GENES, FOXJ2_TARGET_GENES, PBXIP1_TARGET_GENES, SRSF9_TARGET_GENES, DESCARTES_MAIN_FETAL_THYMIC_EPITHELIAL_CELLS, DESCARTES_FETAL_THYMUS_THYMIC_EPITHELIAL_CELLS, ZBED5_TARGET_GENES, ZNF318_TARGET_GENES, chr16p13

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

447 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NPIPB2	UEVLD	Q8IX04	135
NPIPB2	CHDH	Q8NE62	102
NPIPB2	AMOT	Q4VCS5	102
NPIPB2	AMOTL1	Q8IY63	102
NPIPB2	HSPA9	P30036	92
NPIPB2	CARD9	Q9H257	92
NPIPB2	SPNS2	Q8IVW8	91
NPIPB2	CAT	P04040	83
NPIPB2	SRP54	P13624	81
NPIPB2	HAS1	Q92839	80
NPIPB2	HAS3	O00219	80
NPIPB2	HAS2	Q92819	80
NPIPB2	RHBDL3	P58872	71
NPIPB2	DHX9	Q08211	71
NPIPB2	ACP5	P13686	70
NPIPB2	SHMT1	P34896	70

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A0B4J1W7, A0A7H0DN35, A4QN01, A6NHN6, A6NJ64, A8MQ11, E9PIF3, E9PJ23, E9PJI5, E9PKD4, E9PQR5, F5HGC2, F8W1W9, F8WFD2, O75200, O83374, P05913, P06486, P07396, P0C7Q2, P0CK47, P0CK48, P0DM63, P0DXC3, P15489, P16765, P16802, P20969, P36443, P38900, P47003, P68341, P68454, P68455, P87191, P92537, P92561, Q03418, Q32M92, Q4ZGE2

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	18
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1542 predictions. Top by Δscore:

Variant	Effect	Δscore
16:11930558:T:TC	acceptor_gain	1.0000
16:11933515:A:AC	donor_gain	1.0000
16:11933516:C:CC	donor_gain	1.0000
16:11937534:ACTC:A	donor_loss	1.0000
16:11937535:CTCA:C	donor_loss	1.0000
16:11937537:CAC:C	donor_loss	1.0000
16:11937538:A:AC	donor_gain	1.0000
16:11937538:AC:A	donor_gain	1.0000
16:11937539:C:CC	donor_gain	1.0000
16:11937539:CC:C	donor_gain	1.0000
16:11937606:TA:T	donor_gain	1.0000
16:11937607:AA:A	donor_gain	1.0000
16:11937608:A:C	donor_gain	1.0000
16:11937618:TCC:T	donor_gain	1.0000
16:11967566:TTAGG:T	acceptor_loss	1.0000
16:11927878:ACC:A	acceptor_loss	0.9900
16:11927880:C:CA	acceptor_loss	0.9900
16:11927881:T:G	acceptor_loss	0.9900
16:11929383:A:AC	donor_gain	0.9900
16:11929384:C:CC	donor_gain	0.9900
16:11933516:CT:C	donor_gain	0.9900
16:11933533:T:TA	donor_gain	0.9900
16:11933827:T:TA	donor_gain	0.9900
16:11933922:CAA:C	acceptor_gain	0.9900
16:11937538:ACC:A	donor_gain	0.9900
16:11937539:CCC:C	donor_gain	0.9900
16:11937539:CCCA:C	donor_gain	0.9900
16:11937539:CCCAA:C	donor_gain	0.9900
16:11937618:T:TA	donor_gain	0.9900
16:11937665:TAAC:T	acceptor_gain	0.9900

AlphaMissense

2589 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:11929436:A:C	F200L	0.965
16:11929436:A:T	F200L	0.965
16:11929438:A:G	F200L	0.965
16:11933666:A:C	F113L	0.949
16:11933666:A:T	F113L	0.949
16:11933668:A:G	F113L	0.949
16:11937624:A:C	F36L	0.947
16:11937624:A:T	F36L	0.947
16:11937626:A:G	F36L	0.947
16:11937588:A:C	F48L	0.912
16:11937588:A:T	F48L	0.912
16:11937590:A:G	F48L	0.912
16:11933916:G:C	F67L	0.882
16:11933916:G:T	F67L	0.882
16:11933918:A:G	F67L	0.882
16:11933684:C:A	K107N	0.879
16:11933684:C:G	K107N	0.879
16:11929274:A:G	I218T	0.863
16:11937611:A:G	W41R	0.863
16:11937611:A:T	W41R	0.863
16:11929385:T:A	K217N	0.846
16:11929385:T:G	K217N	0.846
16:11930462:A:G	I193T	0.846
16:11927871:C:A	M232I	0.833
16:11927871:C:G	M232I	0.833
16:11927871:C:T	M232I	0.833
16:11927802:T:A	K255N	0.832
16:11927802:T:G	K255N	0.832
16:11929258:T:A	R223S	0.830
16:11929258:T:G	R223S	0.830

dbSNP variants (sampled 300 via entrez): RS1000082883 (16:11974900 C>A,T), RS1000086310 (16:11935943 C>G,T), RS1000100444 (16:11948552 G>A), RS1000150213 (16:11974022 G>C), RS1000152773 (16:11948814 T>C), RS1000155178 (16:11974186 T>C), RS1000181842 (16:11970376 C>G), RS1000323006 (16:11970517 A>G), RS1000331777 (16:11944455 C>T), RS1000371420 (16:11938730 G>A), RS1000433430 (16:11974733 C>T), RS1000494717 (16:11927160 T>C), RS1000568396 (16:11927327 T>C), RS1000579012 (16:11962470 G>A,C), RS1000698684 (16:11934429 T>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (1): desmoplastic small round cell tumor (MONDO:0019373)

Orphanet (1): Desmoplastic small round cell tumor (Orphanet:83469)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D058405	Desmoplastic Small Round Cell Tumor	C04.557.450.795.315

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression	1
perfluorooctanoic acid	increases expression	1
ferrous chloride	decreases expression	1
chloropicrin	increases expression	1
erucylphospho-N,N,N-trimethylpropylammonium	increases expression	1
Ethanol	affects cotreatment, increases abundance, increases expression	1
Gasoline	affects cotreatment, increases abundance, increases expression	1
Polycyclic Aromatic Hydrocarbons	affects cotreatment, increases abundance, increases expression	1
Tunicamycin	increases expression	1
Cadmium Chloride	increases expression	1
Thapsigargin	increases expression	1
1-Butanol	affects cotreatment, increases abundance, increases expression	1
Particulate Matter	affects cotreatment, increases abundance, increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00563680	PHASE2	COMPLETED	QUILT-3.025: A Phase 2 Study of AMG 479 in Relapsed or Refractory Ewing’s Family Tumor and Desmoplastic Small Round Cell Tumors
NCT01125449	PHASE2	WITHDRAWN	Study of High Dose Intravenous (IV) Ascorbic Acid in Measurable Solid Tumor Disease
NCT01946529	PHASE2	ACTIVE_NOT_RECRUITING	Therapeutic Trial for Patients With Ewing Sarcoma Family of Tumor and Desmoplastic Small Round Cell Tumors
NCT02982486	PHASE2	UNKNOWN	A Phase II of Nivolumab Plus Ipilimumab in Non-resectable Sarcoma and Endometrial Carcinoma
NCT04022213	PHASE2	ACTIVE_NOT_RECRUITING	A Study of the Drug I131-Omburtamab in People With Desmoplastic Small Round Cell Tumors and Other Solid Tumors in the Peritoneum
NCT04530487	PHASE2	TERMINATED	Donor Stem Cell Transplant After Chemotherapy for the Treatment of Recurrent or Refractory High-Risk Solid Tumors in Pediatric and Adolescent-Young Adults
NCT06277154	PHASE2	RECRUITING	MASCT-I Combined With Doxorubicin and Ifosfamide for First-line Treatment of Advanced Soft Tissue Sarcoma
NCT06456359	PHASE2	RECRUITING	Pasireotide as Maintenance Treatment in Synovial Sarcoma and Desmoplastic Small Round Cell Tumor
NCT06849986	PHASE2	RECRUITING	IO Combined With AI as First-line Treatment for Patients With Soft Tissue Sarcoma(TAIS)
NCT07328425	PHASE2	RECRUITING	Clinical Study in Adult and Young Adult Patients With Advanced Desmoplastic Small Round Cell Tumor (DSRCT) ISG-TULIPS
NCT00436657	PHASE1	COMPLETED	Continuous Hyperthermic Peritoneal Perfusion (CHPP) With Cisplatin for Children With Peritoneal Cancer
NCT02982941	PHASE1	COMPLETED	Enoblituzumab (MGA271) in Children With B7-H3-expressing Solid Tumors
NCT03600649	PHASE1	UNKNOWN	Clinical Trial of SP-2577 (Seclidemstat) in Patients With Relapsed or Refractory Ewing or Ewing-related Sarcomas
NCT03618381	PHASE1	ACTIVE_NOT_RECRUITING	EGFR806 CAR T Cell Immunotherapy for Recurrent/Refractory Solid Tumors in Children and Young Adults
NCT04483778	PHASE1	ACTIVE_NOT_RECRUITING	B7H3 CAR T Cell Immunotherapy for Recurrent/Refractory Solid Tumors in Children and Young Adults
NCT04897321	PHASE1	RECRUITING	B7-H3-Specific Chimeric Antigen Receptor Autologous T-Cell Therapy for Pediatric Patients With Solid Tumors (3CAR)
NCT04901806	PHASE1	TERMINATED	Study of PBI-200 in Subjects With NTRK-Fusion-Positive Solid Tumors
NCT04095221	PHASE1/PHASE2	COMPLETED	A Study of the Drugs Prexasertib, Irinotecan, and Temozolomide in People With Desmoplastic Small Round Cell Tumor and Rhabdomyosarcoma
NCT04145349	PHASE1/PHASE2	COMPLETED	CAMPFIRE: A Study of Ramucirumab (LY3009806) in Children and Young Adults With Desmoplastic Small Round Cell Tumor
NCT05266196	PHASE1/PHASE2	UNKNOWN	A Rollover Protocol to Allow for Continued Access to the LSD1 Inhibitor Seclidemstat (SP-2577)
NCT05918640	PHASE1/PHASE2	RECRUITING	Lurbinectedin in FET-Fused Tumors
NCT06625190	PHASE1/PHASE2	RECRUITING	Alpha/Beta T and B Cell Depletion With Zoledronic Acid for Solid Tumors
NCT06709495	PHASE1/PHASE2	RECRUITING	Phase 1/2 Trial to Evaluate the Safety and Efficacy of PEEL-224 in Combination With Vincristine and Temozolomide in Adolescents and Young Adults With Relapsed or Refractory Sarcomas
NCT06836505	PHASE1/PHASE2	RECRUITING	Safety and Efficacy of CAR-T Cell Therapy for Relapsed/refractory Neuroblastoma and Desmoplastic Small Round Cell Tumors: a Single-arm, Open-label Trial.
NCT01189643	EARLY_PHASE1	ACTIVE_NOT_RECRUITING	Irinotecan, Temozolomide and Bevacizumab in Combination With Existing High Dose Alkylator Based Chemotherapy for Treatment of Newly Diagnosed Patients With Desmoplastic Small Round Cell Tumor
NCT04213794	EARLY_PHASE1	TERMINATED	Heated Intra-peritoneal Chemotherapy With Doxorubicin and Cisplatin for Abdominal for Pelvic Tumors in Pediatric Patients
NCT02834169	Not specified	UNKNOWN	French National Registry of Rare Peritoneal Surface Malignancies
NCT03874455	Not specified	NO_LONGER_AVAILABLE	Tazemetostat Expanded Access Program for Adults With Solid Tumors
NCT03967834	Not specified	RECRUITING	Multimodal Immune Characterization of RAre Soft Tissue Sarcoma - MIRAS Project From SARRA (SARcome RAre) Project of the French Sarcoma Group
NCT04690374	Not specified	RECRUITING	Registry to Collect Health Information About Desmoplastic Small Round Cell Tumor