NPIPB9

Summary

NPIPB9 (nuclear pore complex interacting protein family member B9, HGNC:41987) is a protein-coding gene on chromosome 16p11.2, encoding Nuclear pore complex-interacting protein family member B9 (F8W1W9).

At a glance

• GWAS associations: 7
• MANE Select transcript: NM_001287250

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:41987
Approved symbol	NPIPB9
Name	nuclear pore complex interacting protein family member B9
Location	16p11.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000196993
Ensembl biotype	protein_coding
Entrez	100507607

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 nonsense_mediated_decay

ENST00000357796, ENST00000550983

RefSeq mRNA: 1 — MANE Select: NM_001287250 NM_001287250

Canonical transcript exons

ENST00000357796 — 7 exons

Exon	Start	End
ENSE00003506341	28766082	28766181
ENSE00003628600	28762251	28762433
ENSE00003687890	28751787	28752592
ENSE00003996625	28766294	28766489
ENSE00003996626	28770588	28770648
ENSE00003996627	28770758	28770793
ENSE00003996628	28772153	28772864

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 79.51.

Top tissues by expression

134 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	79.51	gold quality
left testis	UBERON:0004533	79.01	gold quality
testis	UBERON:0000473	78.07	gold quality
right testis	UBERON:0004534	77.67	gold quality
calcaneal tendon	UBERON:0003701	71.21	gold quality
granulocyte	CL:0000094	71.13	gold quality
corpus callosum	UBERON:0002336	68.46	gold quality
skin of leg	UBERON:0001511	67.65	gold quality
primary visual cortex	UBERON:0002436	67.14	gold quality
right uterine tube	UBERON:0001302	66.90	gold quality
zone of skin	UBERON:0000014	66.73	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	66.59	gold quality
endometrium	UBERON:0001295	66.34	gold quality
stromal cell of endometrium	CL:0002255	65.91	gold quality
mucosa of transverse colon	UBERON:0004991	65.45	gold quality
skin of abdomen	UBERON:0001416	65.40	gold quality
superior frontal gyrus	UBERON:0002661	65.14	gold quality
left ovary	UBERON:0002119	65.13	gold quality
ovary	UBERON:0000992	64.38	gold quality
cerebellar cortex	UBERON:0002129	63.88	gold quality
cerebellum	UBERON:0002037	63.86	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	63.80	gold quality
cerebellar hemisphere	UBERON:0002245	63.71	gold quality
mucosa of stomach	UBERON:0001199	63.08	gold quality
tibial nerve	UBERON:0001323	62.80	gold quality
right ovary	UBERON:0002118	62.72	gold quality
caudate nucleus	UBERON:0001873	62.05	gold quality
hindlimb stylopod muscle	UBERON:0004252	62.05	gold quality
muscle layer of sigmoid colon	UBERON:0035805	62.02	gold quality
right hemisphere of cerebellum	UBERON:0014890	61.99	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.07

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), 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 B9 — F8W1W9 (reviewed: F8W1W9)

All UniProt accessions (2): A0AAK2S2Q9, F8W1W9

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the NPIP family.

RefSeq proteins (1): NP_001274179* (*=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-F8W1W9-F1	49.67	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 1 (showing top): chr16p11

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

599 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NPIPB9	OR10H5	Q8NGA6	577
NPIPB9	FAM229B	Q4G0N7	571
NPIPB9	RABEP2	Q9H5N1	506
NPIPB9	MTRNR2L10	P0CJ77	506
NPIPB9	OR2AK2	Q8NG84	504
NPIPB9	FAM25A	B3EWG3	479
NPIPB9	EIF3CL	B5ME19	451
NPIPB9	WDR31	Q8NA23	447
NPIPB9	OR10H1	Q9Y4A9	447
NPIPB9	TUFM	P49411	431
NPIPB9	EFCAB13	Q8IY85	431
NPIPB9	SULT1A2	P50226	431
NPIPB9	EIF3C	Q99613	423
NPIPB9	TMEM60	Q9H2L4	420
NPIPB9	FAM180B	Q6P0A1	412

IntAct

0 interactions, top by confidence:

BioGRID (3): NPIPB9 (Negative Genetic), NPIPB9 (Negative Genetic), NPIPB9 (Cross-Linking-MS (XL-MS))

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

1093 predictions. Top by Δscore:

Variant	Effect	Δscore
16:28762432:GT:G	donor_gain	1.0000
16:28762434:G:GG	donor_gain	1.0000
16:28766078:CTAG:C	acceptor_loss	1.0000
16:28766081:G:GT	acceptor_loss	1.0000
16:28766081:GGT:G	acceptor_gain	1.0000
16:28766177:GAAAG:G	donor_gain	1.0000
16:28766178:AAAGG:A	donor_loss	1.0000
16:28766180:AGGT:A	donor_loss	1.0000
16:28766181:GGTA:G	donor_loss	1.0000
16:28766182:G:T	donor_loss	1.0000
16:28766183:T:A	donor_loss	1.0000
16:28766490:G:GG	donor_gain	1.0000
16:28770649:G:GG	donor_gain	1.0000
16:28762356:GA:G	donor_gain	0.9900
16:28762429:TTTGT:T	donor_gain	0.9900
16:28762430:TTGT:T	donor_gain	0.9900
16:28766080:A:AG	acceptor_gain	0.9900
16:28766080:AG:A	acceptor_gain	0.9900
16:28766081:G:GG	acceptor_gain	0.9900
16:28766081:GG:G	acceptor_gain	0.9900
16:28766081:GGTGT:G	acceptor_gain	0.9900
16:28766291:AAG:A	acceptor_gain	0.9900
16:28766291:AAGG:A	acceptor_gain	0.9900
16:28766292:A:G	acceptor_gain	0.9900
16:28769457:A:AG	acceptor_gain	0.9900
16:28770792:GG:G	donor_gain	0.9900
16:28770793:GG:G	donor_gain	0.9900
16:28752588:GGAAG:G	donor_gain	0.9800
16:28752589:GAAGG:G	donor_gain	0.9800
16:28752590:AAG:A	donor_loss	0.9800

AlphaMissense

2039 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:28770595:T:C	F200L	0.966
16:28770597:T:A	F200L	0.966
16:28770597:T:G	F200L	0.966
16:28766338:T:C	F147L	0.956
16:28766340:T:A	F147L	0.956
16:28766340:T:G	F147L	0.956
16:28770759:T:C	I218T	0.905
16:28770614:T:C	L206S	0.891
16:28772161:G:A	M232I	0.875
16:28772161:G:C	M232I	0.875
16:28772161:G:T	M232I	0.875
16:28772734:G:C	W423C	0.874
16:28772734:G:T	W423C	0.874
16:28766472:G:C	R191S	0.861
16:28766472:G:T	R191S	0.861
16:28770775:A:C	R223S	0.857
16:28770775:A:T	R223S	0.857
16:28770625:G:C	A210P	0.852
16:28766322:G:C	K141N	0.849
16:28766322:G:T	K141N	0.849
16:28766475:G:C	K192N	0.848
16:28766475:G:T	K192N	0.848
16:28770620:G:C	R208P	0.841
16:28770594:G:A	M199I	0.840
16:28770594:G:C	M199I	0.840
16:28770594:G:T	M199I	0.840
16:28770648:A:C	K217N	0.836
16:28770648:A:T	K217N	0.836
16:28770596:T:C	F200S	0.835
16:28772230:A:C	K255N	0.835

dbSNP variants (sampled 300 via entrez): RS1000541732 (16:28750305 A>G), RS1001161887 (16:28750723 T>C), RS1001212922 (16:28755172 A>G), RS1002213521 (16:28750169 G>A,T), RS1004673084 (16:28754519 A>T), RS1005024360 (16:28752885 C>T), RS1006408886 (16:28771204 T>C), RS1008009554 (16:28769913 C>A,T), RS1008381444 (16:28768916 A>G), RS1008971735 (16:28757406 A>G), RS1009412471 (16:28750562 C>G,T), RS1009438171 (16:28758427 C>G), RS1009940228 (16:28750240 C>A), RS1011252870 (16:28767991 T>C), RS1011366077 (16:28766459 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

7 associations (top):

Study	Trait	p-value
GCST002938_24	Copper levels	4.000000e-06
GCST004131_83	Inflammatory bowel disease	2.000000e-12
GCST004132_69	Crohn’s disease	3.000000e-10
GCST004364_11	Intelligence	4.000000e-08
GCST004364_31	Intelligence	1.000000e-08
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)

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
ethyl-p-hydroxybenzoate	decreases expression	1
abrine	increases expression	1
Acrylamide	increases expression	1
S-Nitrosoglutathione	increases expression	1

Clinical trials (associated diseases)

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