NPIPB13

Summary

NPIPB13 (nuclear pore complex interacting protein family, member B13, HGNC:41989) is a protein-coding gene on chromosome 16p11.2, encoding Nuclear pore complex-interacting protein family member B13 (A6NJU9).

Predicted to be located in membrane.

Source: NCBI Gene 613037 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001395859

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:41989
Approved symbol	NPIPB13
Name	nuclear pore complex interacting protein family, member B13
Location	16p11.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000198064
Ensembl biotype	protein_coding
Entrez	613037

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 10 protein_coding, 3 nonsense_mediated_decay

ENST00000520915, ENST00000562937, ENST00000564219, ENST00000564502, ENST00000568053, ENST00000697092, ENST00000697187, ENST00000697188, ENST00000697189, ENST00000697190, ENST00000697191, ENST00000908420, ENST00000928769

RefSeq mRNA: 4 — MANE Select: NM_001395859 NM_001321892, NM_001395859, NM_001395860, NM_001395861

CCDS: CCDS81968

Canonical transcript exons

ENST00000697092 — 8 exons

Exon	Start	End
ENSE00003458505	30231440	30231635
ENSE00003459637	30245454	30245611
ENSE00003576281	30231748	30231847
ENSE00003588040	30227309	30227369
ENSE00003645530	30245775	30248479
ENSE00003654619	30235451	30235579
ENSE00003685704	30227164	30227199
ENSE00003969482	30222897	30225803

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 96.40.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sural nerve	UBERON:0015488	96.40	gold quality
colonic epithelium	UBERON:0000397	95.45	gold quality
bone marrow cell	CL:0002092	91.12	gold quality
bone marrow	UBERON:0002371	86.46	gold quality
corpus callosum	UBERON:0002336	85.96	gold quality
tonsil	UBERON:0002372	85.76	gold quality
calcaneal tendon	UBERON:0003701	84.54	gold quality
primary visual cortex	UBERON:0002436	84.12	gold quality
hindlimb stylopod muscle	UBERON:0004252	83.96	gold quality
superior frontal gyrus	UBERON:0002661	83.64	gold quality
skeletal muscle tissue	UBERON:0001134	83.44	gold quality
stromal cell of endometrium	CL:0002255	82.53	gold quality
uterine cervix	UBERON:0000002	82.05	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.82	gold quality
right hemisphere of cerebellum	UBERON:0014890	81.47	gold quality
cerebellum	UBERON:0002037	81.06	gold quality
cerebellar cortex	UBERON:0002129	80.88	gold quality
zone of skin	UBERON:0000014	80.83	gold quality
skin of abdomen	UBERON:0001416	80.82	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.69	gold quality
blood	UBERON:0000178	80.66	gold quality
cerebellar hemisphere	UBERON:0002245	80.63	gold quality
skin of leg	UBERON:0001511	80.56	gold quality
liver	UBERON:0002107	80.41	gold quality
thoracic mammary gland	UBERON:0005200	79.98	gold quality
granulocyte	CL:0000094	79.94	gold quality
cortex of kidney	UBERON:0001225	79.93	gold quality
small intestine Peyer’s patch	UBERON:0003454	79.89	gold quality
left ovary	UBERON:0002119	79.47	gold quality
ectocervix	UBERON:0012249	79.40	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	6.47

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

29 targeting NPIPB13, 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-3613-3P	100.00	76.36	7965
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-6759-5P	99.99	66.54	785
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-6793-5P	99.97	65.95	758
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-3934-3P	99.76	65.51	1351
HSA-MIR-17-3P	99.55	66.77	1311
HSA-MIR-330-3P	99.41	69.95	2521
HSA-MIR-6739-3P	99.22	68.84	1843
HSA-MIR-4744	99.01	69.91	1581
HSA-MIR-4742-5P	98.89	68.41	1542
HSA-MIR-4703-5P	98.53	70.13	1645
HSA-MIR-3942-5P	98.52	69.51	1517
HSA-MIR-6771-3P	98.20	66.53	971
HSA-MIR-122-5P	97.23	64.92	1024
HSA-MIR-1288-3P	96.86	66.95	536
HSA-MIR-3169	96.40	67.58	698
HSA-MIR-5195-5P	90.84	65.09	287

Cross-species orthologs

0 orthologs

Paralogs (19): NPIPB12 (ENSG00000169203), NPIPB3 (ENSG00000169246), NPIPA1 (ENSG00000183426), NPIPA5 (ENSG00000183793), NPIPA6 (ENSG00000183889), NPIPB4 (ENSG00000185864), NPIPB15 (ENSG00000196436), NPIPB9 (ENSG00000196993), 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 B13 — A6NJU9 (reviewed: A6NJU9)

All UniProt accessions (10): A6NJU9, A0A1P7U241, A0A8V8TKT1, A0A8V8TKU4, A0A8V8TL61, A0A8V8TM43, A0A8V8TMC5, E5RHP9, F5GWQ4, H3BQU5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the NPIP family.

RefSeq proteins (4): NP_001308821, NP_001382788, NP_001382789, NP_001382790 (=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 (16 total): compositionally biased region 12, region of interest 2, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NJU9-F1	43.87	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 12 (showing top): chr16p11, LU_EZH2_TARGETS_DN, JOHNSTONE_PARVB_TARGETS_3_DN, MIR616_5P, MIR371B_5P, MIR373_5P, MIR6844, MIR4744, MIR3934_3P, JINESH_BLEBBISHIELD_VS_LIVE_CONTROL_UP, JINESH_BLEBBISHIELD_TRANSFORMED_STEM_CELL_SPHERES_DN, TRAVAGLINI_LUNG_NEUTROPHIL_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

699 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NPIPB13	KRTAP5-7	Q6L8G8	574
NPIPB13	DEPDC4	Q8N2C3	447
NPIPB13	KRTAP4-8	Q9BYQ9	444
NPIPB13	MTRNR2L3	P0CJ70	433
NPIPB13	OR1F1	O43749	431
NPIPB13	CSTL1	Q9H114	359
NPIPB13	CCSER2	Q9H7U1	350
NPIPB13	SLC25A47	Q6Q0C1	325
NPIPB13	NWD2	Q9ULI1	321
NPIPB13	CLEC17A	Q6ZS10	316
NPIPB13	PHYHD1	Q5SRE7	307
NPIPB13	OSGEPL1	Q9H4B0	305
NPIPB13	GFOD1	Q9NXC2	305
NPIPB13	ZBTB8OS	Q8IWT0	305
NPIPB13	MIR9-1HG	Q13536	294

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

1 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

861 predictions. Top by Δscore:

Variant	Effect	Δscore
16:30231438:A:AC	donor_gain	1.0000
16:30231439:C:CC	donor_gain	1.0000
16:30231746:ACCTT:A	donor_gain	1.0000
16:30231747:CCTTC:C	donor_gain	1.0000
16:30231750:T:A	donor_gain	1.0000
16:30231845:CAC:C	acceptor_gain	1.0000
16:30235443:ATACT:A	donor_loss	1.0000
16:30235445:ACT:A	donor_loss	1.0000
16:30235446:CTC:C	donor_loss	1.0000
16:30235448:CA:C	donor_loss	1.0000
16:30235449:A:AC	donor_gain	1.0000
16:30235449:AC:A	donor_gain	1.0000
16:30235449:ACC:A	donor_gain	1.0000
16:30235450:C:CT	donor_gain	1.0000
16:30235450:CC:C	donor_gain	1.0000
16:30235450:CCC:C	donor_gain	1.0000
16:30235450:CCCA:C	donor_gain	1.0000
16:30235450:CCCAA:C	donor_gain	1.0000
16:30235529:TCC:T	donor_gain	1.0000
16:30227307:A:AC	donor_gain	0.9900
16:30227308:C:CC	donor_gain	0.9900
16:30228487:T:TC	acceptor_gain	0.9900
16:30231635:CCT:C	acceptor_gain	0.9900
16:30231637:T:C	acceptor_gain	0.9900
16:30231742:CCATA:C	donor_loss	0.9900
16:30231743:CATAC:C	donor_loss	0.9900
16:30231744:ATAC:A	donor_loss	0.9900
16:30231745:TA:T	donor_loss	0.9900
16:30231746:ACC:A	donor_loss	0.9900
16:30231747:C:G	donor_loss	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1005884264 (16:30231803 A>G), RS1006328338 (16:30225448 G>C,T), RS1006560765 (16:30244851 T>A), RS1007722746 (16:30246474 T>C), RS1013897487 (16:30230752 G>A), RS1015941302 (16:30232006 T>G), RS1016007980 (16:30225477 A>G,T), RS1018191438 (16:30246667 C>T), RS1030070923 (16:30245398 C>T), RS1031177352 (16:30232419 G>T), RS1031609589 (16:30246778 G>A), RS1037343252 (16:30244860 T>C,G), RS1037606735 (16:30247276 A>T), RS1043483120 (16:30230479 C>G,T), RS1044975783 (16:30230799 G>A)

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
triphenyl phosphate	affects expression	1
Gallic Acid	increases expression	1
Gasoline	affects cotreatment, increases abundance, increases expression	1
Polycyclic Aromatic Hydrocarbons	increases expression, affects cotreatment, increases abundance	1
Asbestos, Crocidolite	decreases expression	1
Particulate Matter	affects cotreatment, increases abundance, increases expression	1

Clinical trials (associated diseases)

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