NPIPA2

Summary

NPIPA2 (nuclear pore complex interacting protein family member A2, HGNC:41979) is a protein-coding gene on chromosome 16p13.11, encoding Nuclear pore complex-interacting protein family member A2 (E9PIF3).

Predicted to be involved in mRNA transport and protein transport. Predicted to be located in nuclear membrane. Predicted to be part of nuclear pore.

Source: NCBI Gene 642799 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001395485

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:41979
Approved symbol	NPIPA2
Name	nuclear pore complex interacting protein family member A2
Location	16p13.11
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000254852
Ensembl biotype	protein_coding
Entrez	642799

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 5 protein_coding

ENST00000529166, ENST00000530328, ENST00000553201, ENST00000891286, ENST00000956353

RefSeq mRNA: 3 — MANE Select: NM_001395485 NM_001277324, NM_001395485, NM_001395486

CCDS: CCDS59263, CCDS92115

Canonical transcript exons

ENST00000529166 — 10 exons

Exon	Start	End
ENSE00001620155	14762312	14762419
ENSE00001791931	14759210	14759354
ENSE00001799634	14763608	14763643
ENSE00001800644	14763438	14763498
ENSE00002173159	14748028	14748185
ENSE00002324436	14765003	14765462
ENSE00002633878	14758947	14759046
ENSE00002661854	14755192	14755320
ENSE00003966188	14747787	14747865
ENSE00003966190	14742533	14742765

Expression profiles

Bgee: expression breadth ubiquitous, 132 present calls, max score 85.42.

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	85.42	gold quality
left testis	UBERON:0004533	85.31	gold quality
cerebellar hemisphere	UBERON:0002245	85.07	gold quality
cerebellar cortex	UBERON:0002129	84.61	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.49	gold quality
right testis	UBERON:0004534	84.40	gold quality
cerebellum	UBERON:0002037	84.30	gold quality
testis	UBERON:0000473	84.06	gold quality
right uterine tube	UBERON:0001302	80.63	gold quality
apex of heart	UBERON:0002098	80.02	gold quality
adenohypophysis	UBERON:0002196	79.17	gold quality
pituitary gland	UBERON:0000007	78.64	gold quality
muscle layer of sigmoid colon	UBERON:0035805	78.11	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	77.52	gold quality
descending thoracic aorta	UBERON:0002345	77.28	gold quality
lower esophagus muscularis layer	UBERON:0035833	77.20	gold quality
lower esophagus	UBERON:0013473	77.19	gold quality
ascending aorta	UBERON:0001496	77.11	gold quality
thoracic aorta	UBERON:0001515	76.87	gold quality
right lung	UBERON:0002167	76.75	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	76.24	gold quality
right ovary	UBERON:0002118	75.76	gold quality
gastrocnemius	UBERON:0001388	75.64	gold quality
left coronary artery	UBERON:0001626	75.52	gold quality
muscle of leg	UBERON:0001383	75.06	gold quality
tibial artery	UBERON:0007610	74.87	gold quality
mucosa of transverse colon	UBERON:0004991	74.68	gold quality
popliteal artery	UBERON:0002250	74.62	gold quality
right frontal lobe	UBERON:0002810	74.55	gold quality
left ovary	UBERON:0002119	74.49	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.00

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), NPIPA3 (ENSG00000224712), NPIPA9 (ENSG00000233024), NPIPB7 (ENSG00000233232), NPIPB2 (ENSG00000234719), NPIPB5 (ENSG00000243716), NPIPB11 (ENSG00000254206), NPIPB8 (ENSG00000255524)

Protein

Protein identifiers

Nuclear pore complex-interacting protein family member A2 — E9PIF3 (reviewed: E9PIF3)

All UniProt accessions (3): E9PIF3, A0A0B4J2F6, E9PNS9

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the NPIP family.

RefSeq proteins (3): NP_001264253, NP_001382414, NP_001382415 (=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-E9PIF3-F1	52.77	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 2 (showing top): FONG_MCMASTER_OPA1_CARDIOPROTECTION_DN, chr16p13

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

0 interactions, top by confidence:

BioGRID (3): NPIPA2 (Negative Genetic), NPIPA2 (Negative Genetic), 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, 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

996 predictions. Top by Δscore:

Variant	Effect	Δscore
16:14755239:TGG:T	donor_gain	1.0000
16:14755241:G:GT	donor_gain	1.0000
16:14755316:TTTGT:T	donor_gain	1.0000
16:14755317:TTGT:T	donor_gain	1.0000
16:14755317:TTGTG:T	donor_loss	1.0000
16:14755318:TGTGT:T	donor_loss	1.0000
16:14755319:GT:G	donor_gain	1.0000
16:14755321:G:GA	donor_loss	1.0000
16:14755321:G:GG	donor_gain	1.0000
16:14755322:T:TC	donor_loss	1.0000
16:14755324:AGTA:A	donor_loss	1.0000
16:14758942:CCTA:C	acceptor_loss	1.0000
16:14758943:CTA:C	acceptor_loss	1.0000
16:14758944:TA:T	acceptor_loss	1.0000
16:14758945:A:C	acceptor_loss	1.0000
16:14758946:GGT:G	acceptor_gain	1.0000
16:14759021:G:GT	donor_gain	1.0000
16:14759042:GGAAG:G	donor_gain	1.0000
16:14759043:GAAGG:G	donor_gain	1.0000
16:14759044:A:T	donor_gain	1.0000
16:14759045:AGGTA:A	donor_loss	1.0000
16:14759046:GGTAT:G	donor_loss	1.0000
16:14759047:GTAT:G	donor_loss	1.0000
16:14759048:T:G	donor_loss	1.0000
16:14759350:GAACA:G	donor_gain	1.0000
16:14759355:G:GG	donor_gain	1.0000
16:14762310:A:AG	acceptor_gain	1.0000
16:14762310:AGTCT:A	acceptor_gain	1.0000
16:14762311:G:GA	acceptor_gain	1.0000
16:14762311:GT:G	acceptor_gain	1.0000

AlphaMissense

2398 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:14763445:T:C	F204L	0.954
16:14763447:T:A	F204L	0.954
16:14763447:T:G	F204L	0.954
16:14748099:T:C	F12L	0.952
16:14748101:C:A	F12L	0.952
16:14748101:C:G	F12L	0.952
16:14755270:T:C	F67L	0.934
16:14755272:T:A	F67L	0.934
16:14755272:T:G	F67L	0.934
16:14755234:T:C	F55L	0.918
16:14755236:T:A	F55L	0.918
16:14755236:T:G	F55L	0.918
16:14758953:T:C	F86L	0.911
16:14758955:C:A	F86L	0.911
16:14758955:C:G	F86L	0.911
16:14759236:T:C	F126L	0.898
16:14759238:T:A	F126L	0.898
16:14759238:T:G	F126L	0.898
16:14755249:T:A	W60R	0.880
16:14755249:T:C	W60R	0.880
16:14765011:G:A	M236I	0.867
16:14765011:G:C	M236I	0.867
16:14765011:G:T	M236I	0.867
16:14763609:T:C	I222T	0.862
16:14762407:T:C	I197T	0.856
16:14748136:T:C	L24P	0.851
16:14763498:A:C	K221N	0.844
16:14763498:A:T	K221N	0.844
16:14763475:G:C	A214P	0.833
16:14763625:A:C	R227S	0.827

dbSNP variants (sampled 300 via entrez): RS1000383504 (16:14936557 A>G), RS1000581246 (16:14936886 T>C), RS1001315425 (16:14758335 T>C), RS1006824429 (16:14764857 A>C), RS1007775713 (16:14741018 A>C), RS1009545912 (16:14741199 C>T), RS1009628108 (16:14936338 A>G), RS1009785910 (16:14751837 G>A), RS1013450834 (16:14751973 T>C), RS1013484966 (16:14936943 C>T), RS1013691237 (16:14758426 G>A), RS1017952332 (16:14758635 G>A,T), RS1018315630 (16:14764868 G>A,T), RS1019189325 (16:14741114 T>C), RS1020033204 (16:14765027 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

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
chromium hexavalent ion	increases expression	1
Tretinoin	decreases expression	1
Xylitol	increases expression	1
S-Nitrosoglutathione	decreases expression	1

Clinical trials (associated diseases)

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