NPIPB6

Summary

NPIPB6 (nuclear pore complex interacting protein family member B6, HGNC:37454) is a protein-coding gene on chromosome 16p12.1, encoding Nuclear pore complex-interacting protein family member B6 (E9PJ23).

At a glance

• GWAS associations: 6
• MANE Select transcript: NM_001395275

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37454
Approved symbol	NPIPB6
Name	nuclear pore complex interacting protein family member B6
Location	16p12.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000198156
Ensembl biotype	protein_coding
Entrez	728741

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000532254, ENST00000533640, ENST00000695563

RefSeq mRNA: 2 — MANE Select: NM_001395275 NM_001282524, NM_001395275

CCDS: CCDS61892

Canonical transcript exons

ENST00000695563 — 8 exons

Exon	Start	End
ENSE00001718585	28348834	28349029
ENSE00001741950	28344693	28344753
ENSE00001763125	28349142	28349241
ENSE00002141793	28344548	28344583
ENSE00002169404	28352879	28353061
ENSE00003964292	28363023	28363508
ENSE00003964293	28342517	28343188
ENSE00003964294	28362703	28362860

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 91.77.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	91.77	gold quality
right testis	UBERON:0004534	91.46	gold quality
testis	UBERON:0000473	90.55	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.70	gold quality
right uterine tube	UBERON:0001302	74.23	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	70.87	gold quality
ventricular zone	UBERON:0003053	70.14	gold quality
mucosa of transverse colon	UBERON:0004991	69.07	gold quality
cerebellar hemisphere	UBERON:0002245	68.79	gold quality
cerebellar cortex	UBERON:0002129	68.66	gold quality
cerebellum	UBERON:0002037	68.45	gold quality
putamen	UBERON:0001874	68.37	gold quality
right ovary	UBERON:0002118	68.37	gold quality
caudate nucleus	UBERON:0001873	68.09	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	67.57	gold quality
right hemisphere of cerebellum	UBERON:0014890	67.49	gold quality
nucleus accumbens	UBERON:0001882	67.44	gold quality
left ovary	UBERON:0002119	67.43	gold quality
Ammon’s horn	UBERON:0001954	67.26	gold quality
ovary	UBERON:0000992	66.82	gold quality
amygdala	UBERON:0001876	66.73	gold quality
temporal lobe	UBERON:0001871	66.63	gold quality
adenohypophysis	UBERON:0002196	66.09	gold quality
left uterine tube	UBERON:0001303	66.00	gold quality
muscle layer of sigmoid colon	UBERON:0035805	65.96	gold quality
ectocervix	UBERON:0012249	65.63	gold quality
skin of leg	UBERON:0001511	65.56	gold quality
lower esophagus muscularis layer	UBERON:0035833	65.51	gold quality
zone of skin	UBERON:0000014	65.50	gold quality
lower esophagus	UBERON:0013473	65.49	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.19

Regulation

Is transcription factor: no

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), 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 B6 — E9PJ23 (reviewed: E9PJ23)

All UniProt accessions (2): E9PJ23, E9PS57

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the NPIP family.

RefSeq proteins (2): NP_001269453, NP_001382204* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009443	NPIP	Family
IPR054697	NPIP_N	Domain

Pfam: PF06409

UniProt features (4 total): compositionally biased region 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-E9PJ23-F1	52.57	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 2 (showing top): chr16p12, LI_ESTROGENE_BIDIRECTIONAL_E2_RESPONSE

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

641 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NPIPB6	ABHD17C	Q6PCB6	505
NPIPB6	ZKSCAN5	Q9Y2L8	480
NPIPB6	ZNF669	Q96BR6	447
NPIPB6	R3HDM1	Q15032	447
NPIPB6	RMC1	Q96DM3	430
NPIPB6	EIF3CL	B5ME19	420
NPIPB6	TFAP2D	Q7Z6R9	419
NPIPB6	BCDIN3D	Q7Z5W3	419
NPIPB6	MMS22L	Q6ZRQ5	410
NPIPB6	LRRC37B	Q96QE4	406
NPIPB6	GOLGA6A	Q9NYA3	396
NPIPB6	CRTAC1	Q9NQ79	392
NPIPB6	ADPGK	Q9BRR6	380
NPIPB6	PLEKHB1	Q9UF11	370
NPIPB6	ARPP21	Q9UBL0	370

IntAct

2 interactions, top by confidence:

A	B	Type	Score
NPIPB6	GAPDHS	psi-mi:“MI:0914”(association)	0.350

BioGRID (17): NPIPB6 (Affinity Capture-MS), RGPD5 (Affinity Capture-MS), NUP153 (Affinity Capture-MS), RANBP2 (Affinity Capture-MS), KPNB1 (Affinity Capture-MS), NEURL4 (Affinity Capture-MS), CDCA2 (Affinity Capture-MS), IPO7 (Affinity Capture-MS), GAPDHS (Affinity Capture-MS), RGPD8 (Affinity Capture-MS), TRIM27 (Affinity Capture-MS), NCS1 (Affinity Capture-MS), KPNA2 (Affinity Capture-MS), RGPD1 (Affinity Capture-MS), NPIPB6 (Negative Genetic)

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, A0A179HJB8, A4YDT1, C0SPB0, P0C7M7, P39062, Q6P461

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1143 predictions. Top by Δscore:

Variant	Effect	Δscore
16:28344691:A:AC	donor_gain	1.0000
16:28344692:C:CC	donor_gain	1.0000
16:28348832:A:AC	donor_gain	1.0000
16:28348833:C:CC	donor_gain	1.0000
16:28349136:CCATA:C	donor_loss	1.0000
16:28349137:CATA:C	donor_loss	1.0000
16:28349138:ATAC:A	donor_loss	1.0000
16:28349139:TACCT:T	donor_loss	1.0000
16:28349140:A:T	donor_loss	1.0000
16:28349141:C:CA	donor_loss	1.0000
16:28349141:CCTTT:C	donor_gain	1.0000
16:28349239:CAC:C	acceptor_gain	1.0000
16:28349242:CTAG:C	acceptor_loss	1.0000
16:28352877:A:AC	donor_gain	1.0000
16:28352878:C:CC	donor_gain	1.0000
16:28352878:CA:C	donor_gain	1.0000
16:28345881:T:TC	acceptor_gain	0.9900
16:28349028:CCCT:C	acceptor_gain	0.9900
16:28349029:CCT:C	acceptor_gain	0.9900
16:28349031:T:C	acceptor_gain	0.9900
16:28349237:GACAC:G	acceptor_gain	0.9900
16:28349242:C:CC	acceptor_gain	0.9900
16:28352870:TATAC:T	donor_loss	0.9900
16:28352871:ATAC:A	donor_loss	0.9900
16:28352872:TACT:T	donor_loss	0.9900
16:28352873:ACTCA:A	donor_loss	0.9900
16:28352874:CTCAC:C	donor_loss	0.9900
16:28352875:T:TC	donor_loss	0.9900
16:28352876:CACA:C	donor_loss	0.9900
16:28352877:AC:A	donor_loss	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000154744 (16:28356150 A>T), RS1000235342 (16:28355464 T>C), RS1000835662 (16:28347607 A>G), RS1001391507 (16:28350216 G>T), RS1001558142 (16:28347965 C>G,T), RS1001738090 (16:28353406 A>G), RS1002332264 (16:28346702 G>T), RS1003588991 (16:28364733 G>A), RS1004005612 (16:28358252 C>A), RS1004958030 (16:28353152 C>T), RS1005413858 (16:28349998 A>C,T), RS1006008790 (16:28346129 T>C), RS1006369079 (16:28346615 T>C), RS1007004036 (16:28365287 G>A,C), RS1007595388 (16:28342491 A>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST004131_83	Inflammatory bowel disease	2.000000e-12
GCST004132_69	Crohn’s disease	3.000000e-10
GCST005830_10	Hand grip strength	3.000000e-20
GCST008757_46	Alcohol consumption	1.000000e-10
GCST010133_15	Lamb consumption	3.000000e-08
GCST010703_152	Brain morphology (MOSTest)	3.000000e-09

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0006941	grip strength measurement
EFO:0008111	diet measurement
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
sodium arsenite	decreases expression	1
manganese chloride	decreases expression, increases abundance	1
tetrachlorodian	decreases expression	1
2-palmitoylglycerol	increases expression	1
abrine	increases expression	1
Cadmium	decreases expression, increases abundance	1
Manganese	decreases expression, increases abundance	1
Tobacco Smoke Pollution	affects expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	decreases methylation	1
Cadmium Chloride	decreases expression, increases abundance	1
Acrylamide	increases expression	1
S-Nitrosoglutathione	decreases expression	1

Clinical trials (associated diseases)

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