NPIPA3

Summary

NPIPA3 (nuclear pore complex interacting protein family member A3, HGNC:41978) is a protein-coding gene on chromosome 16p13.11, encoding Nuclear pore complex-interacting protein family member A3 (F8WFD2).

At a glance

• MANE Select transcript: NM_001395487

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:41978
Approved symbol	NPIPA3
Name	nuclear pore complex interacting protein family member A3
Location	16p13.11
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000224712
Ensembl biotype	protein_coding
Entrez	642778

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000526520, ENST00000531598, ENST00000552140

RefSeq mRNA: 2 — MANE Select: NM_001395487 NM_001277323, NM_001395487

CCDS: CCDS59262, CCDS92114

Canonical transcript exons

ENST00000531598 — 10 exons

Exon	Start	End
ENSE00001404329	14725883	14726342
ENSE00001625245	14716068	14716196
ENSE00001693748	14724318	14724378
ENSE00001716236	14719827	14719926
ENSE00001758380	14720090	14720234
ENSE00002201184	14724488	14724523
ENSE00002673025	14723192	14723299
ENSE00003966275	14708906	14709063
ENSE00003966277	14708665	14708743
ENSE00003966278	14703411	14703881

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 87.00.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellum	UBERON:0002037	87.00	gold quality
cerebellar cortex	UBERON:0002129	86.97	gold quality
right uterine tube	UBERON:0001302	86.95	gold quality
cerebellar hemisphere	UBERON:0002245	86.90	gold quality
right hemisphere of cerebellum	UBERON:0014890	86.71	gold quality
mucosa of stomach	UBERON:0001199	85.41	gold quality
lower esophagus mucosa	UBERON:0035834	85.03	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.87	gold quality
primary visual cortex	UBERON:0002436	79.66	gold quality
pituitary gland	UBERON:0000007	79.62	gold quality
lower esophagus	UBERON:0013473	78.36	gold quality
lower esophagus muscularis layer	UBERON:0035833	78.32	gold quality
superior frontal gyrus	UBERON:0002661	77.96	gold quality
adenohypophysis	UBERON:0002196	77.62	gold quality
ascending aorta	UBERON:0001496	77.54	gold quality
skeletal muscle tissue	UBERON:0001134	77.50	gold quality
thoracic aorta	UBERON:0001515	77.43	gold quality
muscle layer of sigmoid colon	UBERON:0035805	77.37	gold quality
right frontal lobe	UBERON:0002810	77.18	gold quality
left ovary	UBERON:0002119	76.97	gold quality
right coronary artery	UBERON:0001625	76.61	gold quality
muscle tissue	UBERON:0002385	76.48	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	76.25	gold quality
gastrocnemius	UBERON:0001388	76.18	gold quality
Ammon’s horn	UBERON:0001954	76.05	gold quality
body of uterus	UBERON:0009853	75.91	gold quality
popliteal artery	UBERON:0002250	75.87	gold quality
tibial artery	UBERON:0007610	75.86	gold quality
muscle of leg	UBERON:0001383	75.74	gold quality
apex of heart	UBERON:0002098	75.39	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.13

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), NPIPA9 (ENSG00000233024), NPIPB7 (ENSG00000233232), NPIPB2 (ENSG00000234719), NPIPB5 (ENSG00000243716), NPIPB11 (ENSG00000254206), NPIPA2 (ENSG00000254852), NPIPB8 (ENSG00000255524)

Protein

Protein identifiers

Nuclear pore complex-interacting protein family member A3 — F8WFD2 (reviewed: F8WFD2)

All UniProt accessions (3): F8WFD2, E9PNS9, E9PNV8

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the NPIP family.

RefSeq proteins (2): NP_001264252, NP_001382416* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009443	NPIP	Family
IPR054697	NPIP_N	Domain

Pfam: PF06409

UniProt features (2 total): chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-F8WFD2-F1	52.06	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 1 (showing top): chr16p13

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

842 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NPIPA3	GOLGA6B	A6NDN3	506
NPIPA3	PDXDC1	Q6P996	479
NPIPA3	SMCO3	A2RU48	469
NPIPA3	LRRC37A3	O60309	446
NPIPA3	NUP62	P37198	438
NPIPA3	OR1J4	Q8NGS1	407
NPIPA3	CEP20	Q96NB1	392
NPIPA3	LRRC37A	A6NMS7	378
NPIPA3	AGAP6	Q5VW22	372
NPIPA3	SATL1	Q86VE3	370
NPIPA3	NBPF4	Q96M43	356
NPIPA3	NASP	P49321	350
NPIPA3	MPV17L	Q2QL34	348
NPIPA3	MARF1	Q9Y4F3	328
NPIPA3	CBLL2	Q8N7E2	322
NPIPA3	H3BMD7	H3BMD7	322

IntAct

0 interactions, top by confidence:

BioGRID (1): NPIPA3 (Affinity Capture-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

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

1008 predictions. Top by Δscore:

Variant	Effect	Δscore
16:14716115:TGG:T	donor_gain	1.0000
16:14716117:G:GT	donor_gain	1.0000
16:14716192:TTTGT:T	donor_gain	1.0000
16:14716193:TTGT:T	donor_gain	1.0000
16:14716193:TTGTG:T	donor_loss	1.0000
16:14716195:GT:G	donor_gain	1.0000
16:14716196:TG:T	donor_loss	1.0000
16:14716197:G:C	donor_loss	1.0000
16:14716197:G:GG	donor_gain	1.0000
16:14716198:T:A	donor_loss	1.0000
16:14716200:AG:A	donor_loss	1.0000
16:14719822:CCTA:C	acceptor_loss	1.0000
16:14719823:CTAG:C	acceptor_loss	1.0000
16:14719824:TA:T	acceptor_loss	1.0000
16:14719826:G:GT	acceptor_loss	1.0000
16:14719826:GGT:G	acceptor_gain	1.0000
16:14719901:G:GT	donor_gain	1.0000
16:14719922:GGAAG:G	donor_gain	1.0000
16:14719923:GAAGG:G	donor_gain	1.0000
16:14719924:A:T	donor_gain	1.0000
16:14719924:AAGG:A	donor_loss	1.0000
16:14719926:GGTA:G	donor_loss	1.0000
16:14719927:GTAT:G	donor_loss	1.0000
16:14719928:T:G	donor_loss	1.0000
16:14720230:GAACA:G	donor_gain	1.0000
16:14720235:G:GG	donor_gain	1.0000
16:14723190:A:AG	acceptor_gain	1.0000
16:14723190:AGTCT:A	acceptor_gain	1.0000
16:14723191:G:GC	acceptor_gain	1.0000
16:14723191:GT:G	acceptor_gain	1.0000

AlphaMissense

2398 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:14724325:T:C	F204L	0.954
16:14724327:T:A	F204L	0.954
16:14724327:T:G	F204L	0.954
16:14708977:T:C	F12L	0.952
16:14708979:C:A	F12L	0.952
16:14708979:C:G	F12L	0.952
16:14716146:T:C	F67L	0.934
16:14716148:T:A	F67L	0.934
16:14716148:T:G	F67L	0.934
16:14716110:T:C	F55L	0.918
16:14716112:T:A	F55L	0.918
16:14716112:T:G	F55L	0.918
16:14719833:T:C	F86L	0.911
16:14719835:C:A	F86L	0.911
16:14719835:C:G	F86L	0.911
16:14720116:T:C	F126L	0.898
16:14720118:T:A	F126L	0.898
16:14720118:T:G	F126L	0.898
16:14716125:T:A	W60R	0.880
16:14716125:T:C	W60R	0.880
16:14725891:G:A	M236I	0.867
16:14725891:G:C	M236I	0.867
16:14725891:G:T	M236I	0.867
16:14724489:T:C	I222T	0.862
16:14723287:T:C	I197T	0.856
16:14709014:T:C	L24P	0.851
16:14724378:A:C	K221N	0.844
16:14724378:A:T	K221N	0.844
16:14724355:G:C	A214P	0.833
16:14724505:A:C	R227S	0.827

dbSNP variants (sampled 300 via entrez): RS1002326812 (16:14724200 T>C), RS1003321100 (16:14701957 A>C,T), RS1004983089 (16:14702030 T>A), RS1008731405 (16:14713507 G>A,T), RS1008830821 (16:14712942 C>CA), RS1010515544 (16:14724090 C>G), RS1010568067 (16:14718627 T>C), RS1015169207 (16:14725516 G>C), RS1016080481 (16:14702043 G>A), RS1021982713 (16:14718782 A>G), RS1022036062 (16:14713033 G>A,C), RS1028889773 (16:14712920 G>T), RS1029357651 (16:14702211 G>A), RS1030602495 (16:14712969 T>C), RS1030885773 (16:14718531 A>G)

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

11 total (human), top 11 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression	1
ethyl-p-hydroxybenzoate	decreases expression	1
chromium hexavalent ion	increases expression	1
Leflunomide	decreases expression	1
Allergens	affects cotreatment, decreases expression, increases abundance	1
Vehicle Emissions	affects cotreatment, decreases expression, increases abundance	1
Cadmium	decreases expression, increases abundance	1
Tretinoin	decreases expression	1
Cadmium Chloride	decreases expression, increases abundance	1
S-Nitrosoglutathione	increases expression	1
Particulate Matter	affects cotreatment, decreases expression, increases abundance	1

Clinical trials (associated diseases)

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