NPIPA9

Summary

NPIPA9 (nuclear pore complex interacting protein family member A9, HGNC:41984) is a protein-coding gene on chromosome 16p12.3, encoding Nuclear pore complex-interacting protein family member A9 (A0A0B4J1W7).

At a glance

• MANE Select transcript: NM_001405004

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:41984
Approved symbol	NPIPA9
Name	nuclear pore complex interacting protein family member A9
Location	16p12.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000233024
Ensembl biotype	protein_coding
Entrez	105376752

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding, 2 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000327792, ENST00000427999, ENST00000526166, ENST00000528301, ENST00000531453, ENST00000533010, ENST00000543228, ENST00000545114, ENST00000546267

RefSeq mRNA: 2 — MANE Select: NM_001405004 NM_001401710, NM_001405004

CCDS: CCDS92118

Canonical transcript exons

ENST00000427999 — 10 exons

Exon	Start	End
ENSE00001644947	18376736	18376839
ENSE00001681998	18361170	18361277
ENSE00001688624	18360093	18360153
ENSE00001715994	18359948	18359983
ENSE00001764925	18372723	18372854
ENSE00002163343	18358090	18358588
ENSE00003501612	18368258	18368386
ENSE00003578732	18374832	18375069
ENSE00003669626	18364535	18364634
ENSE00003684737	18364227	18364371

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 99.63.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar hemisphere	UBERON:0002245	99.63	gold quality
cerebellar cortex	UBERON:0002129	99.60	gold quality
right hemisphere of cerebellum	UBERON:0014890	99.58	gold quality
cerebellum	UBERON:0002037	99.52	gold quality
right uterine tube	UBERON:0001302	99.45	gold quality
adenohypophysis	UBERON:0002196	99.39	gold quality
lower esophagus mucosa	UBERON:0035834	99.24	gold quality
pituitary gland	UBERON:0000007	99.21	gold quality
right ovary	UBERON:0002118	98.60	gold quality
mucosa of stomach	UBERON:0001199	98.53	gold quality
right frontal lobe	UBERON:0002810	98.49	gold quality
sural nerve	UBERON:0015488	98.47	gold quality
corpus callosum	UBERON:0002336	98.46	gold quality
left ovary	UBERON:0002119	98.40	gold quality
body of uterus	UBERON:0009853	98.29	gold quality
ovary	UBERON:0000992	98.19	gold quality
body of pancreas	UBERON:0001150	98.04	gold quality
tibial nerve	UBERON:0001323	97.92	gold quality
fallopian tube	UBERON:0003889	97.76	gold quality
muscle layer of sigmoid colon	UBERON:0035805	97.76	gold quality
smooth muscle tissue	UBERON:0001135	97.71	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	97.68	gold quality
descending thoracic aorta	UBERON:0002345	97.61	gold quality
lower esophagus	UBERON:0013473	97.57	gold quality
lower esophagus muscularis layer	UBERON:0035833	97.57	gold quality
anterior cingulate cortex	UBERON:0009835	97.48	gold quality
Ammon’s horn	UBERON:0001954	97.38	gold quality
mucosa of transverse colon	UBERON:0004991	97.37	gold quality
left uterine tube	UBERON:0001303	97.35	gold quality
Brodmann (1909) area 9	UBERON:0013540	97.33	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.79

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

Protein

Protein identifiers

Nuclear pore complex-interacting protein family member A9 — A0A0B4J1W7 (reviewed: A0A0B4J1W7)

All UniProt accessions (3): A0A0B4J1W7, H0YF59, Q9NRE7

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the NPIP family.

RefSeq proteins (2): NP_001388639, NP_001391933* (*=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-A0A0B4J1W7-F1	50.59	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 2 (showing top): chr16p12, PAF1_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

447 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NPIPA9	UEVLD	Q8IX04	135
NPIPA9	CHDH	Q8NE62	102
NPIPA9	AMOT	Q4VCS5	102
NPIPA9	AMOTL1	Q8IY63	102
NPIPA9	HSPA9	P30036	92
NPIPA9	CARD9	Q9H257	92
NPIPA9	SPNS2	Q8IVW8	91
NPIPA9	CAT	P04040	83
NPIPA9	SRP54	P13624	81
NPIPA9	HAS1	Q92839	80
NPIPA9	HAS3	O00219	80
NPIPA9	HAS2	Q92819	80
NPIPA9	RHBDL3	P58872	71
NPIPA9	DHX9	Q08211	71
NPIPA9	ACP5	P13686	70
NPIPA9	SHMT1	P34896	70

IntAct

0 interactions, top by confidence:

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

0 predictions. Top by Δscore:

AlphaMissense

2400 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:18360144:A:C	F185L	0.969
16:18360144:A:T	F185L	0.969
16:18360146:A:G	F185L	0.969
16:18368342:A:C	F36L	0.935
16:18368342:A:T	F36L	0.935
16:18368344:A:G	F36L	0.935
16:18368306:A:C	F48L	0.927
16:18368306:A:T	F48L	0.927
16:18368308:A:G	F48L	0.927
16:18361182:A:G	I178T	0.917
16:18364343:A:C	F107L	0.917
16:18364343:A:T	F107L	0.917
16:18364345:A:G	F107L	0.917
16:18368329:A:G	W41R	0.903
16:18368329:A:T	W41R	0.903
16:18358580:C:A	M217I	0.888
16:18358580:C:G	M217I	0.888
16:18358580:C:T	M217I	0.888
16:18364626:G:C	F67L	0.881
16:18364626:G:T	F67L	0.881
16:18364628:A:G	F67L	0.881
16:18361182:A:T	I178K	0.861
16:18359982:A:G	I203T	0.855
16:18360093:T:A	K202N	0.852
16:18360093:T:G	K202N	0.852
16:18360145:A:G	F185S	0.844
16:18361216:C:G	A167P	0.842
16:18361182:A:C	I178R	0.835
16:18364620:C:A	K69N	0.832
16:18364620:C:G	K69N	0.832

dbSNP variants (sampled 300 via entrez): RS1001067255 (16:18375045 G>A), RS1006153988 (16:18374477 G>A,C,T), RS1012267341 (16:18364657 T>C), RS1012697636 (16:18375022 G>A), RS1014130990 (16:18374738 A>G), RS1015954368 (16:18371548 A>G), RS1015988762 (16:18367575 A>G), RS1020788330 (16:18374497 G>A), RS1023819792 (16:18374765 C>G,T), RS1025792506 (16:18371566 T>A), RS1028642669 (16:18367296 C>T), RS1029361009 (16:18371430 C>A,G,T), RS1030811629 (16:18365183 A>T), RS1032523952 (16:18375134 C>G,T), RS1035881972 (16:18374660 C>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

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
abrine	increases expression	1
Vehicle Emissions	increases abundance, decreases expression	1
Okadaic Acid	increases expression	1
S-Nitrosoglutathione	increases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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