NPIPB11

Summary

NPIPB11 (nuclear pore complex interacting protein family member B11, HGNC:37453) is a protein-coding gene on chromosome 16p11.2, encoding Nuclear pore complex-interacting protein family member B11 (E5RHQ5).

Predicted to act upstream of or within prevention of polyspermy. Predicted to be located in external side of plasma membrane and sperm head plasma membrane.

Source: NCBI Gene 728888 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 4 total
• MANE Select transcript: NM_001310137

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37453
Approved symbol	NPIPB11
Name	nuclear pore complex interacting protein family member B11
Location	16p11.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000254206
Ensembl biotype	protein_coding
Entrez	728888

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000524087, ENST00000614927, ENST00000698511

RefSeq mRNA: 1 — MANE Select: NM_001310137 NM_001310137

CCDS: CCDS92131

Canonical transcript exons

ENST00000644019 — 0 exons

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 82.77.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.77	gold quality
right hemisphere of cerebellum	UBERON:0014890	80.81	gold quality
right lobe of liver	UBERON:0001114	80.70	gold quality
cerebellar hemisphere	UBERON:0002245	80.15	gold quality
cerebellar cortex	UBERON:0002129	80.09	gold quality
cerebellum	UBERON:0002037	79.95	gold quality
granulocyte	CL:0000094	79.78	gold quality
mucosa of transverse colon	UBERON:0004991	79.19	gold quality
right uterine tube	UBERON:0001302	78.86	gold quality
spleen	UBERON:0002106	78.49	gold quality
left ovary	UBERON:0002119	78.39	gold quality
cortex of kidney	UBERON:0001225	78.01	gold quality
right ovary	UBERON:0002118	77.88	gold quality
ovary	UBERON:0000992	77.34	gold quality
small intestine Peyer’s patch	UBERON:0003454	77.26	gold quality
right frontal lobe	UBERON:0002810	77.09	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	76.45	silver quality
skin of abdomen	UBERON:0001416	76.18	gold quality
omental fat pad	UBERON:0010414	76.17	gold quality
sural nerve	UBERON:0015488	76.08	gold quality
apex of heart	UBERON:0002098	75.84	gold quality
lower esophagus mucosa	UBERON:0035834	75.81	gold quality
primary visual cortex	UBERON:0002436	75.72	gold quality
subcutaneous adipose tissue	UBERON:0002190	75.65	gold quality
adipose tissue	UBERON:0001013	75.64	gold quality
left uterine tube	UBERON:0001303	75.59	gold quality
zone of skin	UBERON:0000014	75.47	gold quality
skin of leg	UBERON:0001511	75.47	gold quality
metanephros cortex	UBERON:0010533	75.32	gold quality
transverse colon	UBERON:0001157	75.31	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.32
E-CURD-10	no	53.08

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

9 targeting NPIPB11, 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-12131	99.48	68.72	1673
HSA-MIR-6739-3P	99.22	68.84	1843
HSA-MIR-122-5P	97.23	64.92	1024

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), NPIPB2 (ENSG00000234719), NPIPB5 (ENSG00000243716), NPIPA2 (ENSG00000254852), NPIPB8 (ENSG00000255524)

Protein

Protein identifiers

Nuclear pore complex-interacting protein family member B11 — E5RHQ5 (reviewed: E5RHQ5)

All UniProt accessions (2): A0A087WV59, E5RHQ5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the NPIP family.

RefSeq proteins (1): NP_001297066* (*=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 (14 total): compositionally biased region 10, region of interest 2, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-E5RHQ5-F1	40.73	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 9 (showing top): chr16p11, MIR656_3P, MIR6844, MIR3934_3P, MIR6793_5P, JINESH_BLEBBISHIELD_VS_LIVE_CONTROL_UP, JINESH_BLEBBISHIELD_TRANSFORMED_STEM_CELL_SPHERES_DN, HOEK_NK_CELL_2011_2012_TIV_ADULT_1DY_UP, HE_LIM_SUN_FETAL_LUNG_C1_SMG_CELL

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

825 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NPIPB11	GOLGA6B	A6NDN3	507
NPIPB11	LRRC37A3	O60309	447
NPIPB11	NUP62	P37198	438
NPIPB11	ZFAND1	Q8TCF1	400
NPIPB11	LRRC37A	A6NMS7	380
NPIPB11	AGAP6	Q5VW22	375
NPIPB11	NBPF4	Q96M43	358
NPIPB11	NASP	P49321	352
NPIPB11	BOLA2	Q9H3K6	348
NPIPB11	PDXDC1	Q6P996	348
NPIPB11	INO80E	Q8NBZ0	348
NPIPB11	TMEM219	Q86XT9	336
NPIPB11	OR7D2	Q96RA2	336
NPIPB11	VCF2	Q5XKR9	322
NPIPB11	DIP2C	Q9Y2E4	316

IntAct

0 interactions, top by confidence:

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1001 predictions. Top by Δscore:

Variant	Effect	Δscore
16:29389939:A:AC	donor_gain	1.0000
16:29389940:C:CC	donor_gain	1.0000
16:29390247:ACCTT:A	donor_gain	1.0000
16:29390248:CCTTC:C	donor_gain	1.0000
16:29390251:T:A	donor_gain	1.0000
16:29390346:CAC:C	acceptor_gain	1.0000
16:29390349:CTAGG:C	acceptor_loss	1.0000
16:29393940:ATACT:A	donor_loss	1.0000
16:29393942:ACTC:A	donor_loss	1.0000
16:29393943:CTCA:C	donor_loss	1.0000
16:29393944:TCACC:T	donor_loss	1.0000
16:29393946:A:AC	donor_gain	1.0000
16:29393946:AC:A	donor_gain	1.0000
16:29393946:ACC:A	donor_gain	1.0000
16:29393947:C:CC	donor_gain	1.0000
16:29393947:CC:C	donor_gain	1.0000
16:29393947:CCC:C	donor_gain	1.0000
16:29393947:CCCA:C	donor_gain	1.0000
16:29393947:CCCAA:C	donor_gain	1.0000
16:29394026:TCC:T	donor_gain	1.0000
16:29385793:A:AC	donor_gain	0.9900
16:29385794:C:CC	donor_gain	0.9900
16:29386979:T:TC	acceptor_gain	0.9900
16:29389940:CT:C	donor_gain	0.9900
16:29390136:CCT:C	acceptor_gain	0.9900
16:29390138:T:C	acceptor_gain	0.9900
16:29390243:CCATA:C	donor_loss	0.9900
16:29390244:CATA:C	donor_loss	0.9900
16:29390245:ATAC:A	donor_loss	0.9900
16:29390246:TA:T	donor_loss	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000106608 (16:29401726 G>C), RS1000311965 (16:29407204 C>A,G,T), RS1000389092 (16:29397161 ACT>A), RS1000672527 (16:29383214 G>A,T), RS1000688345 (16:29407029 G>A), RS1000844812 (16:29392544 T>G), RS1000875660 (16:29392350 G>A), RS1000995899 (16:29398599 G>A), RS1001108197 (16:29402888 A>G), RS1001349213 (16:29391923 G>A,T), RS1001425689 (16:29397946 C>A,T), RS1001444922 (16:29397317 C>T), RS1001475731 (16:29397196 G>C), RS1001810545 (16:29407365 A>C), RS1001923034 (16:29402072 T>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

1 associations (top):

Study	Trait	p-value
GCST006948_67	Feeling nervous	4.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009597	feeling nervous measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Particulate Matter	affects cotreatment, increases abundance, increases expression	2
aristolochic acid I	increases expression	1
mancozeb	increases expression	1
sodium arsenite	decreases expression	1
manganese chloride	decreases expression, increases abundance	1
chloropicrin	increases expression	1
Ethanol	affects cotreatment, increases abundance, increases expression	1
Cadmium	decreases expression, increases abundance	1
Gasoline	affects cotreatment, increases abundance, increases expression	1
Manganese	decreases expression, increases abundance	1
Polycyclic Aromatic Hydrocarbons	affects cotreatment, increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tunicamycin	increases expression	1
Cadmium Chloride	decreases expression, increases abundance	1
1-Butanol	affects cotreatment, increases abundance, increases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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