NPIPB8

Summary

NPIPB8 (nuclear pore complex interacting protein family member B8, HGNC:37490) is a protein-coding gene on chromosome 16p11.2, encoding Nuclear pore complex-interacting protein family member B8 (E9PQR5).

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 2 total
• MANE Select transcript: NM_001310136

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37490
Approved symbol	NPIPB8
Name	nuclear pore complex interacting protein family member B8
Location	16p11.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000255524
Ensembl biotype	protein_coding
Entrez	728734

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000526428, ENST00000529716, ENST00000683297

RefSeq mRNA: 2 — MANE Select: NM_001310136 NM_001310136, NM_001385922

CCDS: CCDS81963

Canonical transcript exons

ENST00000683297 — 8 exons

Exon	Start	End
ENSE00002145710	28651957	28652056
ENSE00002154265	28656463	28656523
ENSE00002179896	28648135	28648317
ENSE00002183441	28656633	28656668
ENSE00002198386	28652169	28652364
ENSE00003916186	28638065	28638150
ENSE00003921791	28658028	28658744
ENSE00003922118	28638323	28638480

Expression profiles

Bgee: expression breadth ubiquitous, 127 present calls, max score 79.86.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.86	silver quality
left testis	UBERON:0004533	79.10	gold quality
testis	UBERON:0000473	78.32	gold quality
right testis	UBERON:0004534	78.21	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	76.76	silver quality
stromal cell of endometrium	CL:0002255	65.50	gold quality
mucosa of transverse colon	UBERON:0004991	64.61	gold quality
cortical plate	UBERON:0005343	61.54	gold quality
duodenum	UBERON:0002114	60.50	gold quality
tonsil	UBERON:0002372	57.80	gold quality
cerebellum	UBERON:0002037	55.02	gold quality
cerebellar cortex	UBERON:0002129	54.86	gold quality
granulocyte	CL:0000094	54.51	gold quality
cerebellar hemisphere	UBERON:0002245	54.48	gold quality
apex of heart	UBERON:0002098	54.44	gold quality
right hemisphere of cerebellum	UBERON:0014890	53.47	gold quality
right coronary artery	UBERON:0001625	53.11	gold quality
left ovary	UBERON:0002119	53.00	gold quality
right ovary	UBERON:0002118	52.97	gold quality
skin of leg	UBERON:0001511	52.09	gold quality
ovary	UBERON:0000992	51.94	gold quality
right lobe of thyroid gland	UBERON:0001119	51.82	gold quality
tibial nerve	UBERON:0001323	51.36	gold quality
zone of skin	UBERON:0000014	51.26	gold quality
transverse colon	UBERON:0001157	51.25	gold quality
colonic epithelium	UBERON:0000397	51.10	silver quality
ectocervix	UBERON:0012249	50.85	gold quality
skeletal muscle tissue	UBERON:0001134	50.55	gold quality
uterine cervix	UBERON:0000002	50.54	gold quality
muscle layer of sigmoid colon	UBERON:0035805	50.51	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.02

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), NPIPB6 (ENSG00000198156), NPIPA8 (ENSG00000214940), NPIPA7 (ENSG00000214967), NPIPA3 (ENSG00000224712), NPIPA9 (ENSG00000233024), NPIPB7 (ENSG00000233232), NPIPB2 (ENSG00000234719), NPIPB5 (ENSG00000243716), NPIPB11 (ENSG00000254206), NPIPA2 (ENSG00000254852)

Protein

Protein identifiers

Nuclear pore complex-interacting protein family member B8 — E9PQR5 (reviewed: E9PQR5)

All UniProt accessions (2): E9PQR5, H0YDQ7

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the NPIP family.

RefSeq proteins (2): NP_001297065, NP_001372851 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009443	NPIP	Family
IPR054697	NPIP_N	Domain

Pfam: PF06409

UniProt features (6 total): compositionally biased region 3, region of interest 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-E9PQR5-F1	52.40	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 10 (showing top): chr16p11, HES2_TARGET_GENES, IGLV5_37_TARGET_GENES, KMT2D_TARGET_GENES, LHX9_TARGET_GENES, LHX2_TARGET_GENES, DNMT3A_TARGET_GENES, HOEK_B_CELL_2011_2012_TIV_ADULT_1DY_UP, HOEK_PBMC_INACTIVATED_INFLUENZA_ADULT_3DY_UP, GENES_CORRELATED_WITH_RICTOR_DELETION

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

579 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NPIPB8	OR10H5	Q8NGA6	605
NPIPB8	C2orf74	A8MZ97	529
NPIPB8	OR10H1	Q9Y4A9	506
NPIPB8	EFCAB13	Q8IY85	477
NPIPB8	H0YL38	H0YL38	445
NPIPB8	ZNF280D	Q6N043	435
NPIPB8	MALRD1	Q5VYJ5	430
NPIPB8	APOL4	Q9BPW4	418
NPIPB8	RABEP2	Q9H5N1	398
NPIPB8	SYS1	Q8N2H4	397
NPIPB8	APOBR	Q0VD83	366
NPIPB8	CLN3	Q13286	366
NPIPB8	HMG20A	Q9NP66	356
NPIPB8	DEXI	O95424	348
NPIPB8	MSANTD1	Q6ZTZ1	320

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1235 predictions. Top by Δscore:

Variant	Effect	Δscore
16:28651952:CCTA:C	acceptor_loss	1.0000
16:28651954:TA:T	acceptor_loss	1.0000
16:28651955:A:AC	acceptor_loss	1.0000
16:28651956:GGT:G	acceptor_gain	1.0000
16:28652052:GAAAG:G	donor_gain	1.0000
16:28652053:AAAG:A	donor_loss	1.0000
16:28652054:AAGG:A	donor_loss	1.0000
16:28652055:AGGTA:A	donor_loss	1.0000
16:28652056:GGTAT:G	donor_loss	1.0000
16:28652057:G:A	donor_loss	1.0000
16:28652058:T:A	donor_loss	1.0000
16:28652365:G:GG	donor_gain	1.0000
16:28656524:G:GG	donor_gain	1.0000
16:28638478:AAGGT:A	donor_loss	0.9900
16:28638479:AGG:A	donor_loss	0.9900
16:28638482:T:A	donor_loss	0.9900
16:28648240:GA:G	donor_gain	0.9900
16:28648316:GT:G	donor_gain	0.9900
16:28648318:G:GG	donor_gain	0.9900
16:28651955:A:AG	acceptor_gain	0.9900
16:28651956:G:GG	acceptor_gain	0.9900
16:28651956:GGTGT:G	acceptor_gain	0.9900
16:28652166:AAG:A	acceptor_gain	0.9900
16:28652166:AAGG:A	acceptor_gain	0.9900
16:28652167:A:G	acceptor_gain	0.9900
16:28652362:ACA:A	donor_gain	0.9900
16:28655334:A:AG	acceptor_gain	0.9900
16:28656667:GG:G	donor_gain	0.9900
16:28656668:GG:G	donor_gain	0.9900
16:28656668:GGT:G	donor_loss	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000022197 (16:28652979 G>C), RS1000115233 (16:28652567 G>A), RS1000290041 (16:28636703 A>G), RS1000297066 (16:28640995 C>T), RS1000567276 (16:28641107 C>T), RS1001138221 (16:28644032 G>C), RS1001529869 (16:28640630 G>A), RS1001618007 (16:28640928 A>AT), RS1001647163 (16:28647826 G>A), RS1001717702 (16:28635912 C>A,T), RS1001799851 (16:28637869 A>C), RS1001909718 (16:28651755 A>C), RS1002343423 (16:28636171 T>A,C), RS1002509388 (16:28643698 T>C), RS1002640556 (16:28640210 C>T)

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

7 associations (top):

Study	Trait	p-value
GCST004131_83	Inflammatory bowel disease	2.000000e-12
GCST004132_69	Crohn’s disease	3.000000e-10
GCST005316_467	Intelligence (MTAG)	1.000000e-09
GCST006269_378	General cognitive ability	1.000000e-10
GCST006269_758	General cognitive ability	5.000000e-09
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:0004337	intelligence
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)

PharmGKB clinical annotations

3 annotations.

Variant	Type	Level	Drugs	Phenotypes
rs28374453	Metabolism/PK	3	tapentadol
rs28374453	Metabolism/PK	3	desmethylnaproxen
rs28374453	Metabolism/PK	3	acetaminophen

PharmGKB variants

7 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs750155	NPIPB8, SULT1A1		0.00	0
rs1059491	NPIPB8, SULT1A2		0.00	0
rs1136703	NPIPB8, SULT1A2		0.00	0
rs1801030	NPIPB8, SULT1A1, SULT1A2		0.00	0
rs3760091	NPIPB8, SULT1A1		0.00	0
rs8049439	ATXN2L, IL27, NPIPB8		0.00	0
rs28374453	NPIPB8, SULT1A1	3	0.00	3	tapentadol;acetaminophen;desmethylnaproxen

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
2-palmitoylglycerol	increases expression	1
abrine	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Ethanol	affects cotreatment, increases abundance, increases expression	1
Cadmium	decreases expression, increases abundance	1
Copper	affects cotreatment, decreases expression	1
Gasoline	affects cotreatment, increases abundance, increases expression	1
Polycyclic Aromatic Hydrocarbons	increases expression, affects cotreatment, increases abundance	1
Cadmium Chloride	decreases expression, increases abundance	1
Particulate Matter	affects cotreatment, increases abundance, increases expression	1

Clinical trials (associated diseases)

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