NPIPA1

Summary

NPIPA1 (nuclear pore complex interacting protein family member A1, HGNC:7909) is a protein-coding gene on chromosome 16p13.11, encoding Nuclear pore complex-interacting protein family member A1 (Q9UND3).

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 9284 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 51 total — 1 likely-pathogenic
• MANE Select transcript: NM_006985

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:7909
Approved symbol	NPIPA1
Name	nuclear pore complex interacting protein family member A1
Location	16p13.11
Locus type	gene with protein product
Status	Approved
Aliases	morpheus
Ensembl gene	ENSG00000183426
Ensembl biotype	protein_coding
OMIM	606406
Entrez	9284

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 4 protein_coding, 4 protein_coding_CDS_not_defined, 2 retained_intron

ENST00000328085, ENST00000424549, ENST00000472413, ENST00000534720, ENST00000537062, ENST00000541836, ENST00000545479, ENST00000545831, ENST00000663682, ENST00000967088

RefSeq mRNA: 1 — MANE Select: NM_006985 NM_006985

CCDS: CCDS10557

Canonical transcript exons

ENST00000328085 — 8 exons

Exon	Start	End
ENSE00001683943	14937443	14937505
ENSE00001893648	14951615	14952056
ENSE00003485216	14948930	14949037
ENSE00003584157	14945574	14945673
ENSE00003616089	14941812	14941940
ENSE00003636291	14945837	14945981
ENSE00003640684	14950050	14950110
ENSE00003659908	14950220	14950255

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 99.86.

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	99.86	gold quality
cerebellar cortex	UBERON:0002129	99.85	gold quality
cerebellar hemisphere	UBERON:0002245	99.85	gold quality
cerebellum	UBERON:0002037	99.84	gold quality
pituitary gland	UBERON:0000007	99.52	gold quality
adenohypophysis	UBERON:0002196	99.51	gold quality
right testis	UBERON:0004534	99.34	gold quality
primary visual cortex	UBERON:0002436	99.33	gold quality
left testis	UBERON:0004533	99.31	gold quality
right frontal lobe	UBERON:0002810	99.28	gold quality
right uterine tube	UBERON:0001302	99.22	gold quality
right ovary	UBERON:0002118	99.13	gold quality
left ovary	UBERON:0002119	99.08	gold quality
lower esophagus muscularis layer	UBERON:0035833	98.95	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	98.95	gold quality
lower esophagus	UBERON:0013473	98.94	gold quality
muscle layer of sigmoid colon	UBERON:0035805	98.94	gold quality
Ammon’s horn	UBERON:0001954	98.92	gold quality
superior frontal gyrus	UBERON:0002661	98.92	gold quality
tibial nerve	UBERON:0001323	98.90	gold quality
ovary	UBERON:0000992	98.88	gold quality
body of uterus	UBERON:0009853	98.87	gold quality
mucosa of stomach	UBERON:0001199	98.82	gold quality
amygdala	UBERON:0001876	98.80	gold quality
hypothalamus	UBERON:0001898	98.76	gold quality
temporal lobe	UBERON:0001871	98.75	gold quality
endocervix	UBERON:0000458	98.74	gold quality
left uterine tube	UBERON:0001303	98.71	gold quality
anterior cingulate cortex	UBERON:0009835	98.68	gold quality
right lobe of thyroid gland	UBERON:0001119	98.60	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.86

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Paralogs (19): NPIPB12 (ENSG00000169203), NPIPB3 (ENSG00000169246), 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), NPIPA2 (ENSG00000254852), NPIPB8 (ENSG00000255524)

Protein

Protein identifiers

Nuclear pore complex-interacting protein family member A1 — Q9UND3 (reviewed: Q9UND3)

Alternative names: Nuclear pore complex-interacting protein

All UniProt accessions (3): Q9UND3, F8WB45, H0YH09

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. May associate with the nuclear pore complex.

Subcellular location. Nucleus. Nuclear pore complex. Nucleus membrane.

Tissue specificity. Widely expressed.

Similarity. Belongs to the NPIP family.

RefSeq proteins (1): NP_008916* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR009443	NPIP	Family
IPR054697	NPIP_N	Domain

Pfam: PF06409

UniProt features (9 total): sequence conflict 6, chain 1, region of interest 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UND3-F1	51.61	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 80 (showing top): KANG_DOXORUBICIN_RESISTANCE_UP, PEREZ_TP63_TARGETS, HSIAO_HOUSEKEEPING_GENES, ONKEN_UVEAL_MELANOMA_UP, GOBP_NUCLEOBASE_CONTAINING_COMPOUND_TRANSPORT, AMIT_EGF_RESPONSE_20_HELA, PEREZ_TP53_AND_TP63_TARGETS, SCHLOSSER_SERUM_RESPONSE_AUGMENTED_BY_MYC, GOBP_RNA_LOCALIZATION, GOCC_NUCLEAR_ENVELOPE, LAIHO_COLORECTAL_CANCER_SERRATED_DN, GOCC_NUCLEAR_PORE, GOCC_NUCLEAR_MEMBRANE, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, POMEROY_MEDULLOBLASTOMA_PROGNOSIS_UP

GO Biological Process (2): protein transport (GO:0015031), mRNA transport (GO:0051028)

GO Molecular Function (0):

GO Cellular Component (4): nuclear pore (GO:0005643), nuclear membrane (GO:0031965), nucleus (GO:0005634), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nuclear envelope	2
transport	1
intracellular protein localization	1
establishment of protein localization	1
RNA transport	1
nuclear protein-containing complex	1
nucleus	1
organelle membrane	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1039 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NPIPA1	NUP62	P37198	886
NPIPA1	PPP3R1	P06705	391
NPIPA1	PDXDC1	Q6P996	369
NPIPA1	GOLGA6B	A6NDN3	355
NPIPA1	LGR5	O75473	307
NPIPA1	LRRC37A	A6NMS7	287
NPIPA1	GAPDH	P00354	287
NPIPA1	NBPF11	Q86T75	287
NPIPA1	LRRC37A3	O60309	273
NPIPA1	PTPRC	P08575	247
NPIPA1	MPV17L	Q2QL34	244
NPIPA1	GOLGA6A	Q9NYA3	231
NPIPA1	TBL1X	O60907	226
NPIPA1	CD4	P01730	223
NPIPA1	H3BMD7	H3BMD7	222
NPIPA1	ACTB	P02570	222

IntAct

2 interactions, top by confidence:

A	B	Type	Score
FOS	NPIPA1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (9): NPIPA1 (Affinity Capture-RNA), NPIPA1 (Affinity Capture-MS), NPIPA1 (Negative Genetic), NPIPA2 (Negative Genetic), NPIPA1 (Negative Genetic), NPIPA2 (Negative Genetic), NPIPA3 (Affinity Capture-MS), NPIPA1 (Affinity Capture-RNA), NPIPA1 (Affinity Capture-RNA)

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	1
Uncertain significance	43
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
503580	GRCh37/hg19 16p13.11(chr16:14968859-16291983)x3	Likely pathogenic

SpliceAI

997 predictions. Top by Δscore:

Variant	Effect	Δscore
16:14941859:TGG:T	donor_gain	1.0000
16:14941861:G:GT	donor_gain	1.0000
16:14941936:TTTGT:T	donor_gain	1.0000
16:14941937:TTGT:T	donor_gain	1.0000
16:14941938:TGTG:T	donor_loss	1.0000
16:14941939:GT:G	donor_gain	1.0000
16:14941940:TG:T	donor_loss	1.0000
16:14941941:G:GG	donor_gain	1.0000
16:14941943:G:GT	donor_loss	1.0000
16:14941944:AGTAT:A	donor_loss	1.0000
16:14945571:TAGGT:T	acceptor_loss	1.0000
16:14945572:A:G	acceptor_loss	1.0000
16:14945573:G:A	acceptor_loss	1.0000
16:14945573:GGT:G	acceptor_gain	1.0000
16:14945648:G:GT	donor_gain	1.0000
16:14945669:GGAAG:G	donor_gain	1.0000
16:14945670:G:GT	donor_gain	1.0000
16:14945671:A:T	donor_gain	1.0000
16:14945964:G:GT	donor_gain	1.0000
16:14945977:GAACA:G	donor_gain	1.0000
16:14945982:G:GG	donor_gain	1.0000
16:14948928:A:AG	acceptor_gain	1.0000
16:14948929:G:GG	acceptor_gain	1.0000
16:14948929:GTCT:G	acceptor_gain	1.0000
16:14949038:G:GG	donor_gain	1.0000
16:14950111:G:GG	donor_gain	1.0000
16:14937592:G:GT	donor_gain	0.9900
16:14937596:G:GT	donor_gain	0.9900
16:14941806:TTCCA:T	acceptor_loss	0.9900
16:14941807:TCCA:T	acceptor_loss	0.9900

AlphaMissense

2278 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:14950057:T:C	F185L	0.971
16:14950059:T:A	F185L	0.971
16:14950059:T:G	F185L	0.971
16:14941890:T:C	F48L	0.939
16:14941892:T:A	F48L	0.939
16:14941892:T:G	F48L	0.939
16:14941854:T:C	F36L	0.936
16:14941856:T:A	F36L	0.936
16:14941856:T:G	F36L	0.936
16:14941869:T:A	W41R	0.917
16:14941869:T:C	W41R	0.917
16:14945580:T:C	F67L	0.914
16:14945582:C:A	F67L	0.914
16:14945582:C:G	F67L	0.914
16:14949025:T:C	I178T	0.914
16:14945863:T:C	F107L	0.909
16:14945865:T:A	F107L	0.909
16:14945865:T:G	F107L	0.909
16:14950087:G:C	A195P	0.889
16:14950221:T:C	I203T	0.888
16:14950110:A:C	K202N	0.885
16:14950110:A:T	K202N	0.885
16:14951623:G:A	M217I	0.882
16:14951623:G:C	M217I	0.882
16:14951623:G:T	M217I	0.882
16:14949025:T:A	I178K	0.872
16:14948991:G:C	A167P	0.871
16:14950058:T:C	F185S	0.866
16:14945588:G:C	K69N	0.865
16:14945588:G:T	K69N	0.865

dbSNP variants (sampled 300 via entrez): RS1000383504 (16:14936557 A>G), RS1000581246 (16:14936886 T>C), RS1006163452 (16:14939777 C>T), RS1006195987 (16:14943963 A>T), RS1007193736 (16:14935581 G>A,C), RS1007391776 (16:14936046 A>G), RS1009285969 (16:14935637 C>A,T), RS1009628108 (16:14936338 A>G), RS1012064652 (16:14950094 A>C), RS1013100755 (16:14938939 T>C), RS1013484966 (16:14936943 C>T), RS1017656116 (16:14939859 A>C,G), RS1017983699 (16:14944111 T>C), RS1018589495 (16:14935590 C>G,T), RS1020729679 (16:14936508 A>G)

Disease associations

OMIM: gene MIM:606406 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST009391_2072	Metabolite levels	3.000000e-08
GCST012051_6	Systolic blood pressure	6.000000e-07

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0010347	cholesteryl ester 20:3 measurement
EFO:0006335	systolic blood pressure

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

37 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Tretinoin	decreases expression	2
Particulate Matter	increases abundance, increases expression, affects cotreatment	2
aristolochic acid I	increases expression	1
bisphenol F	affects cotreatment, decreases expression	1
dicrotophos	increases expression	1
bufotalin	decreases expression	1
bisphenol A	affects cotreatment, decreases expression	1
2-butenal	decreases expression	1
manganese chloride	decreases expression, increases abundance	1
tamibarotene	decreases expression	1
chromium hexavalent ion	increases expression	1
ICG 001	increases expression	1
bisphenol S	affects cotreatment, decreases expression	1
Leflunomide	decreases expression	1
Acetaminophen	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Ethanol	affects cotreatment, increases abundance, increases expression	1
Cadmium	decreases expression	1
Cisplatin	affects reaction, decreases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Diethylhexyl Phthalate	decreases expression	1
Doxorubicin	decreases expression	1
Gasoline	affects cotreatment, increases abundance, increases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Lead	affects expression	1
Manganese	increases abundance, decreases expression	1
Methyl Methanesulfonate	increases expression	1
Piroxicam	affects reaction, decreases expression	1
Polycyclic Aromatic Hydrocarbons	increases expression, affects cotreatment, increases abundance	1
Tobacco Smoke Pollution	decreases expression	1

Clinical trials (associated diseases)

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