NPIPB12

Summary

NPIPB12 (nuclear pore complex interacting protein family member B12, HGNC:37491) is a protein-coding gene on chromosome 16p11.2, encoding Nuclear pore complex-interacting protein family member B12 (F8W0I5).

Predicted to be located in membrane.

Source: NCBI Gene 440353 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001395931

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37491
Approved symbol	NPIPB12
Name	nuclear pore complex interacting protein family member B12
Location	16p11.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000169203
Ensembl biotype	protein_coding
Entrez	440353

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 nonsense_mediated_decay, 3 protein_coding, 1 retained_intron

ENST00000547235, ENST00000548346, ENST00000549733, ENST00000550665, ENST00000550690, ENST00000551448, ENST00000552123, ENST00000878929, ENST00000938250

RefSeq mRNA: 3 — MANE Select: NM_001395931 NM_001355401, NM_001395931, NM_001395932

Canonical transcript exons

ENST00000550665 — 8 exons

Exon	Start	End
ENSE00002339863	29483534	29485833
ENSE00002405550	29505784	29506408
ENSE00002407228	29505473	29505630
ENSE00003491982	29491775	29491874
ENSE00003575657	29495479	29495607
ENSE00003624709	29491467	29491662
ENSE00003642886	29487339	29487399
ENSE00003668597	29487194	29487229

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 99.10.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	99.10	gold quality
right uterine tube	UBERON:0001302	99.05	gold quality
granulocyte	CL:0000094	99.00	gold quality
cerebellar hemisphere	UBERON:0002245	98.96	gold quality
lower esophagus mucosa	UBERON:0035834	98.96	gold quality
cerebellar cortex	UBERON:0002129	98.93	gold quality
sural nerve	UBERON:0015488	98.85	gold quality
mucosa of stomach	UBERON:0001199	98.82	gold quality
cerebellum	UBERON:0002037	98.81	gold quality
mucosa of transverse colon	UBERON:0004991	98.80	gold quality
spleen	UBERON:0002106	98.78	gold quality
metanephros cortex	UBERON:0010533	98.65	gold quality
right testis	UBERON:0004534	98.61	gold quality
right frontal lobe	UBERON:0002810	98.58	gold quality
small intestine Peyer’s patch	UBERON:0003454	98.58	gold quality
skin of abdomen	UBERON:0001416	98.49	gold quality
skin of leg	UBERON:0001511	98.45	gold quality
zone of skin	UBERON:0000014	98.42	gold quality
left testis	UBERON:0004533	98.37	gold quality
pituitary gland	UBERON:0000007	98.35	gold quality
right lobe of liver	UBERON:0001114	98.34	gold quality
Ammon’s horn	UBERON:0001954	98.34	gold quality
transverse colon	UBERON:0001157	98.21	gold quality
left lobe of thyroid gland	UBERON:0001120	98.18	gold quality
amygdala	UBERON:0001876	98.18	gold quality
adenohypophysis	UBERON:0002196	98.17	gold quality
left uterine tube	UBERON:0001303	98.15	gold quality
temporal lobe	UBERON:0001871	98.11	gold quality
right ovary	UBERON:0002118	98.08	gold quality
subcutaneous adipose tissue	UBERON:0002190	98.08	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.97
E-ENAD-17	no	184.50

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Paralogs (19): 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), NPIPB8 (ENSG00000255524)

Protein

Protein identifiers

Nuclear pore complex-interacting protein family member B12 — F8W0I5 (reviewed: F8W0I5)

All UniProt accessions (6): F8W0I5, E5RHP9, F5GWQ4, H0YIK9, H0YIQ3, H0YIQ5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the NPIP family.

RefSeq proteins (3): NP_001342330, NP_001382860, NP_001382861 (=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 (10 total): compositionally biased region 6, region of interest 2, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-F8W0I5-F1	44.73	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 8 (showing top): chr16p11, JINESH_BLEBBISHIELD_VS_LIVE_CONTROL_UP, JINESH_BLEBBISHIELD_TRANSFORMED_STEM_CELL_SPHERES_DN, DESCARTES_MAIN_FETAL_RETINAL_PIGMENT_CELLS, DESCARTES_FETAL_CEREBELLUM_VASCULAR_ENDOTHELIAL_CELLS, HOEK_T_CELL_2011_2012_TIV_ADULT_7DY_UP, HOEK_T_CELL_2011_2012_TIV_ADULT_1DY_UP, GENES_CORRELATED_WITH_MYC_DELETION

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

623 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NPIPB12	DEPDC4	Q8N2C3	505
NPIPB12	KRTAP4-8	Q9BYQ9	479
NPIPB12	MTRNR2L3	P0CJ70	476
NPIPB12	KRTAP5-7	Q6L8G8	448
NPIPB12	CCSER2	Q9H7U1	392
NPIPB12	NWD2	Q9ULI1	361
NPIPB12	CLEC17A	Q6ZS10	358
NPIPB12	ZBTB8OS	Q8IWT0	348
NPIPB12	PHYHD1	Q5SRE7	333
NPIPB12	GXYLT1	Q4G148	322
NPIPB12	NIBAN3	Q86XR2	321
NPIPB12	SGSM1	Q2NKQ1	320
NPIPB12	PCDHB9	Q9Y5E1	317
NPIPB12	CDC42EP1	Q00587	316
NPIPB12	DDX51	Q8N8A6	311

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

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

350 predictions. Top by Δscore:

Variant	Effect	Δscore
16:29487337:A:AC	donor_gain	1.0000
16:29487338:C:CC	donor_gain	1.0000
16:29485832:ACCTG:A	acceptor_loss	0.9900
16:29485834:C:CA	acceptor_loss	0.9900
16:29485835:T:A	acceptor_loss	0.9900
16:29487187:AACTT:A	donor_loss	0.9800
16:29487192:A:AC	donor_gain	0.9800
16:29487192:AC:A	donor_gain	0.9800
16:29487193:C:CC	donor_gain	0.9800
16:29487193:CC:C	donor_gain	0.9800
16:29485829:CTGAC:C	acceptor_gain	0.9700
16:29487338:CTTTG:C	donor_gain	0.9700
16:29485834:C:CC	acceptor_gain	0.9500
16:29487193:CCCA:C	donor_gain	0.9400
16:29487193:CCCAG:C	donor_gain	0.9400
16:29487333:CCTTA:C	donor_loss	0.9400
16:29487334:CTTAC:C	donor_loss	0.9400
16:29487335:TTAC:T	donor_loss	0.9400
16:29487336:T:TG	donor_loss	0.9400
16:29487337:A:AG	donor_loss	0.9400
16:29487338:CT:C	donor_gain	0.9400
16:29487331:CTCCT:C	donor_loss	0.9300
16:29487332:TCCTT:T	donor_loss	0.9300
16:29487034:CACGG:C	donor_gain	0.9200
16:29487036:CGG:C	donor_gain	0.9200
16:29487038:G:C	donor_gain	0.9100
16:29485843:C:T	acceptor_gain	0.8900
16:29487546:CAGT:C	donor_gain	0.8900
16:29487228:ATCTG:A	acceptor_loss	0.8800
16:29487229:TCTGA:T	acceptor_loss	0.8800

AlphaMissense

3851 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1003472224 (16:29497755 C>G), RS1003608244 (16:29495019 C>T), RS1005166021 (16:29499304 C>A,T), RS1010915699 (16:29492777 A>G,T), RS1011301459 (16:29485627 C>T), RS1012323413 (16:29499142 T>A), RS1012767784 (16:29505893 T>G), RS1012864331 (16:29492456 A>C), RS1015155980 (16:29499326 A>G), RS1015187304 (16:29507286 C>T), RS1020945928 (16:29493016 C>T), RS1021041961 (16:29486944 C>T), RS1027911425 (16:29495114 G>C), RS1028275209 (16:29499153 G>C,T), RS1029366039 (16:29504567 A>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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Gasoline	affects cotreatment, increases abundance, increases expression	1
Polycyclic Aromatic Hydrocarbons	affects cotreatment, increases abundance, increases expression	1
Smoke	increases abundance, increases expression	1
Particulate Matter	affects cotreatment, increases abundance, increases expression	1

Clinical trials (associated diseases)

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