NPIPB5

Summary

NPIPB5 (nuclear pore complex interacting protein family member B5, HGNC:37233) is a protein-coding gene on chromosome 16p12.2, encoding Nuclear pore complex-interacting protein family member B5 (A8MRT5).

Predicted to be located in membrane.

Source: NCBI Gene 100132247 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 160 total — 1 pathogenic, 1 likely-pathogenic
• MANE Select transcript: NM_001395849

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37233
Approved symbol	NPIPB5
Name	nuclear pore complex interacting protein family member B5
Location	16p12.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000243716
Ensembl biotype	protein_coding
Entrez	100132247

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 9 protein_coding, 7 nonsense_mediated_decay, 4 protein_coding_CDS_not_defined, 4 retained_intron

ENST00000356156, ENST00000415654, ENST00000415833, ENST00000424340, ENST00000442450, ENST00000517347, ENST00000517539, ENST00000521555, ENST00000528249, ENST00000536620, ENST00000538509, ENST00000538590, ENST00000539604, ENST00000539929, ENST00000540704, ENST00000541154, ENST00000541664, ENST00000542518, ENST00000543407, ENST00000543997, ENST00000544308, ENST00000545375, ENST00000546168, ENST00000621622

RefSeq mRNA: 4 — MANE Select: NM_001395849 NM_001135865, NM_001395849, NM_001395850, NM_001395851

CCDS: CCDS45443

Canonical transcript exons

ENST00000424340 — 7 exons

Exon	Start	End
ENSE00003476942	22527778	22527973
ENSE00003480851	22527566	22527665
ENSE00003490573	22532060	22532120
ENSE00003682048	22532230	22532265
ENSE00003689297	22523820	22523948
ENSE00003978241	22510891	22513921
ENSE00003978242	22533626	22536535

Expression profiles

Bgee: expression breadth ubiquitous, 250 present calls, max score 99.62.

FANTOM5 (CAGE): breadth broad, TPM avg 0.4632 / max 54.2742, expressed in 234 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
207812	0.4632	234

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	99.62	gold quality
right hemisphere of cerebellum	UBERON:0014890	99.61	gold quality
cerebellar hemisphere	UBERON:0002245	99.52	gold quality
cerebellar cortex	UBERON:0002129	99.49	gold quality
left lobe of thyroid gland	UBERON:0001120	99.41	gold quality
skin of abdomen	UBERON:0001416	99.37	gold quality
metanephros cortex	UBERON:0010533	99.36	gold quality
mucosa of stomach	UBERON:0001199	99.34	gold quality
small intestine Peyer’s patch	UBERON:0003454	99.33	gold quality
right lobe of thyroid gland	UBERON:0001119	99.32	gold quality
skin of leg	UBERON:0001511	99.31	gold quality
granulocyte	CL:0000094	99.26	gold quality
endocervix	UBERON:0000458	99.24	gold quality
tibial nerve	UBERON:0001323	99.21	gold quality
right frontal lobe	UBERON:0002810	99.20	gold quality
right ovary	UBERON:0002118	99.19	gold quality
left ovary	UBERON:0002119	99.18	gold quality
left testis	UBERON:0004533	99.18	gold quality
transverse colon	UBERON:0001157	99.16	gold quality
ectocervix	UBERON:0012249	99.16	gold quality
minor salivary gland	UBERON:0001830	99.15	gold quality
adenohypophysis	UBERON:0002196	99.14	gold quality
muscle layer of sigmoid colon	UBERON:0035805	99.14	gold quality
cerebellum	UBERON:0002037	99.11	gold quality
right testis	UBERON:0004534	99.11	gold quality
body of uterus	UBERON:0009853	99.09	gold quality
lower esophagus mucosa	UBERON:0035834	99.06	gold quality
body of pancreas	UBERON:0001150	99.05	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	99.02	gold quality
left uterine tube	UBERON:0001303	99.01	gold quality

Single-cell (SCXA)

Detected in 9 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-MTAB-9067	yes	13.02
E-ANND-3	yes	9.75
E-MTAB-6678	yes	7.03
E-CURD-88	yes	4.23
E-CURD-135	no	783.76
E-MTAB-8911	no	258.78
E-CURD-11	no	240.69
E-MTAB-6108	no	56.53
E-CURD-112	no	2.15

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

8 targeting NPIPB5, 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-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), NPIPB11 (ENSG00000254206), NPIPA2 (ENSG00000254852), NPIPB8 (ENSG00000255524)

Protein

Protein identifiers

Nuclear pore complex-interacting protein family member B5 — A8MRT5 (reviewed: A8MRT5)

All UniProt accessions (11): A8MRT5, A0A087WXW0, E5RHP9, E9PKP1, F5GWQ4, F5GXZ6, F5GYP3, F5GZP9, F6SDX0, H0YIL3, U3KRG3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the NPIP family.

RefSeq proteins (4): NP_001129337, NP_001382778, NP_001382779, NP_001382780 (=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 (15 total): compositionally biased region 9, region of interest 3, chain 1, transmembrane region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A8MRT5-F1	44.71	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 10 (showing top): DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN, chr16p12, MIR656_3P, MIR6844, MIR3934_3P, MIR6793_5P, MANNO_MIDBRAIN_NEUROTYPES_HENDO, HU_FETAL_RETINA_RPE, DESCARTES_MAIN_FETAL_CSH1_CSH2_POSITIVE_CELLS, DAZARD_RESPONSE_TO_UV_NHEK_DN

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

685 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NPIPB5	DEPDC4	Q8N2C3	448
NPIPB5	KRTAP4-8	Q9BYQ9	446
NPIPB5	MTRNR2L3	P0CJ70	436
NPIPB5	KRTAP5-7	Q6L8G8	419
NPIPB5	CCSER2	Q9H7U1	357
NPIPB5	NWD2	Q9ULI1	326
NPIPB5	CLEC17A	Q6ZS10	322
NPIPB5	PHYHD1	Q5SRE7	311
NPIPB5	OSGEPL1	Q9H4B0	307
NPIPB5	GFOD1	Q9NXC2	307
NPIPB5	ZBTB8OS	Q8IWT0	306
NPIPB5	GXYLT1	Q4G148	294
NPIPB5	RBMXL2	O75526	290
NPIPB5	NIBAN3	Q86XR2	290
NPIPB5	SGSM1	Q2NKQ1	290

IntAct

3 interactions, top by confidence:

A	B	Type	Score
rep	NPIPB5	psi-mi:“MI:0915”(physical association)	0.490

BioGRID (4): NPIPB5 (Affinity Capture-RNA), NPIPB5 (Two-hybrid), NPIPB5 (Two-hybrid), NPIPB5 (Affinity Capture-MS)

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

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	1
Uncertain significance	147
Likely benign	10
Benign	0

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
1703534	GRCh37/hg19 16p12.2(chr16:21801889-22710614)	Pathogenic
3024600	GRCh37/hg19 16p12.2(chr16:21771791-22659880)x1	Likely pathogenic

SpliceAI

934 predictions. Top by Δscore:

Variant	Effect	Δscore
16:22523867:TGG:T	donor_gain	1.0000
16:22523944:TTTGG:T	donor_gain	1.0000
16:22523945:TTGG:T	donor_gain	1.0000
16:22523946:TGG:T	donor_gain	1.0000
16:22523947:GG:G	donor_gain	1.0000
16:22523947:GGG:G	donor_gain	1.0000
16:22523948:GG:G	donor_gain	1.0000
16:22523949:G:GA	donor_loss	1.0000
16:22523949:G:GG	donor_gain	1.0000
16:22523950:TGA:T	donor_loss	1.0000
16:22523951:GAGTA:G	donor_loss	1.0000
16:22527565:GGT:G	acceptor_gain	1.0000
16:22527661:GGAAG:G	donor_gain	1.0000
16:22527662:GAAGG:G	donor_gain	1.0000
16:22527663:A:T	donor_gain	1.0000
16:22527974:G:GG	donor_gain	1.0000
16:22532121:G:GG	donor_gain	1.0000
16:22523810:A:AG	acceptor_gain	0.9900
16:22523811:T:G	acceptor_gain	0.9900
16:22523814:TTCCA:T	acceptor_loss	0.9900
16:22523815:TCCAG:T	acceptor_loss	0.9900
16:22523816:CCA:C	acceptor_loss	0.9900
16:22523817:CA:C	acceptor_loss	0.9900
16:22523818:A:AC	acceptor_loss	0.9900
16:22523818:A:AG	acceptor_gain	0.9900
16:22523819:G:GA	acceptor_gain	0.9900
16:22523819:GGTT:G	acceptor_gain	0.9900
16:22523869:G:GT	donor_gain	0.9900
16:22527562:CTA:C	acceptor_loss	0.9900
16:22527563:TAGGT:T	acceptor_loss	0.9900

AlphaMissense

7287 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:22535304:T:A	I774K	0.999
16:22535430:T:A	I816K	0.999
16:22535052:T:A	I690K	0.998
16:22535178:T:A	I732K	0.998
16:22535396:T:C	F805L	0.998
16:22535398:C:A	F805L	0.998
16:22535398:C:G	F805L	0.998
16:22535430:T:G	I816R	0.998
16:22535556:T:A	I858K	0.998
16:22535018:T:C	F679L	0.997
16:22535020:C:A	F679L	0.997
16:22535020:C:G	F679L	0.997
16:22535144:T:C	F721L	0.997
16:22535146:C:A	F721L	0.997
16:22535146:C:G	F721L	0.997
16:22535213:T:C	F744L	0.997
16:22535214:T:C	F744S	0.997
16:22535215:C:A	F744L	0.997
16:22535215:C:G	F744L	0.997
16:22535270:T:C	F763L	0.997
16:22535272:C:A	F763L	0.997
16:22535272:C:G	F763L	0.997
16:22535304:T:G	I774R	0.997
16:22535361:T:A	I793N	0.997
16:22535466:T:C	F828S	0.997
16:22535484:T:A	I834K	0.997
16:22535487:T:A	I835N	0.997
16:22535522:T:C	F847L	0.997
16:22535524:C:A	F847L	0.997
16:22535524:C:G	F847L	0.997

dbSNP variants (sampled 300 via entrez): RS1004803656 (16:22536885 A>G,T), RS1005093068 (16:22529614 G>A), RS1008986428 (16:22529365 C>T), RS1020960 (16:22535893 C>T), RS1024158834 (16:22529652 C>T), RS1027481557 (16:22510735 G>A,C), RS1027596153 (16:22529606 A>C), RS1039018908 (16:22529395 G>A,C,T), RS1042575684 (16:22529158 T>C), RS1042912264 (16:22530230 C>T), RS1049102744 (16:22536599 G>A,C), RS1054006988 (16:22528724 G>A,C,T), RS111270574 (16:22523079 C>A), RS111504279 (16:22520880 C>T), RS111522977 (16:22530046 C>T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:611913

GenCC curated gene-disease

Mondo (1): proximal 16p11.2 microdeletion syndrome (MONDO:0012756)

Orphanet (1): Proximal 16p11.2 microdeletion syndrome (Orphanet:261197)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C579850	16p11.2 Deletion Syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Particulate Matter	decreases expression, increases expression	2
aristolochic acid I	increases expression	1
bisphenol F	affects cotreatment, decreases expression	1
alpha-pinene	affects cotreatment, decreases expression, increases abundance	1
bisphenol A	decreases expression, affects cotreatment	1
manganese chloride	increases abundance, decreases expression	1
methacrylaldehyde	affects cotreatment, decreases expression, increases abundance	1
bisphenol S	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Acrolein	affects cotreatment, decreases expression, increases abundance	1
Air Pollutants	affects cotreatment, decreases expression, increases abundance	1
Copper	affects cotreatment, decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Manganese	decreases expression, increases abundance	1
Ozone	affects cotreatment, decreases expression, increases abundance	1
Silicon Dioxide	increases expression	1
Dronabinol	increases expression	1
Tunicamycin	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Acrylamide	increases expression	1
Volatile Organic Compounds	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT04271332	PHASE2	ACTIVE_NOT_RECRUITING	Safety, Tolerability, and Efficacy of Arbaclofen in 16p11.2 Deletion
NCT01238250	Not specified	RECRUITING	Online Study of People Who Have Genetic Changes and Features of Autism: Simons Searchlight