NUP107

Summary

NUP107 (nucleoporin 107, HGNC:29914) is a protein-coding gene on chromosome 12q15, encoding Nuclear pore complex protein Nup107 (P57740). Plays a role in the nuclear pore complex (NPC) assembly and/or maintenance. It is a common-essential gene (DepMap: required in 93.5% of cancer cell lines).

This gene encodes a member of the nucleoporin family. The protein is localized to the nuclear rim and is an essential component of the nuclear pore complex (NPC). All molecules entering or leaving the nucleus either diffuse through or are actively transported by the NPC. Alternate transcriptional splice variants of this gene have been observed but have not been thoroughly characterized.

Source: NCBI Gene 57122 — RefSeq curated summary.

At a glance

• Gene–disease (curated): nephrotic syndrome, type 11 (Strong, GenCC) — +5 more curated relationships
• GWAS associations: 1
• Clinical variants (ClinVar): 418 total — 13 pathogenic, 13 likely-pathogenic
• Phenotypes (HPO): 97
• Cancer dependency (DepMap): dependent in 93.5% of screened cell lines (common-essential)
• MANE Select transcript: NM_020401

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29914
Approved symbol	NUP107
Name	nucleoporin 107
Location	12q15
Locus type	gene with protein product
Status	Approved
Aliases	NUP84
Ensembl gene	ENSG00000111581
Ensembl biotype	protein_coding
OMIM	607617
Entrez	57122

Gene structure

Transcript identifiers

Ensembl transcripts: 29 — 20 protein_coding, 4 retained_intron, 3 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay

ENST00000229179, ENST00000378905, ENST00000401003, ENST00000535333, ENST00000535718, ENST00000537598, ENST00000537662, ENST00000538549, ENST00000538993, ENST00000539373, ENST00000539906, ENST00000540453, ENST00000545140, ENST00000908483, ENST00000908484, ENST00000908485, ENST00000908486, ENST00000908487, ENST00000908488, ENST00000908489, ENST00000920335, ENST00000920336, ENST00000920337, ENST00000920338, ENST00000920339, ENST00000920340, ENST00000966547, ENST00000966548, ENST00000966549

RefSeq mRNA: 2 — MANE Select: NM_020401 NM_001330192, NM_020401

CCDS: CCDS81712, CCDS8985

Canonical transcript exons

ENST00000229179 — 28 exons

Exon	Start	End
ENSE00002296804	68742355	68745809
ENSE00002321492	68686978	68687073
ENSE00003466817	68700726	68700853
ENSE00003477962	68691968	68692112
ENSE00003500749	68702736	68702784
ENSE00003510548	68721841	68721986
ENSE00003511249	68734708	68734833
ENSE00003511591	68731607	68731719
ENSE00003557265	68741813	68741980
ENSE00003558196	68732637	68732739
ENSE00003559195	68731110	68731260
ENSE00003571134	68726499	68726617
ENSE00003587429	68690631	68690746
ENSE00003588348	68696819	68696922
ENSE00003616692	68710005	68710093
ENSE00003626963	68689533	68689619
ENSE00003627276	68721118	68721177
ENSE00003629498	68719578	68719654
ENSE00003638498	68709238	68709309
ENSE00003639561	68713730	68713808
ENSE00003650487	68722104	68722152
ENSE00003654421	68725727	68725796
ENSE00003660185	68735231	68735344
ENSE00003661617	68727351	68727389
ENSE00003670267	68688962	68689053
ENSE00003677328	68733452	68733612
ENSE00003680519	68719341	68719431
ENSE00003689051	68715627	68715740

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 97.50.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.8813 / max 1036.5043, expressed in 1788 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
126608	24.8813	1788

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	97.50	gold quality
oocyte	CL:0000023	95.89	gold quality
ventricular zone	UBERON:0003053	95.89	gold quality
calcaneal tendon	UBERON:0003701	95.64	gold quality
tendon	UBERON:0000043	94.25	gold quality
embryo	UBERON:0000922	93.56	gold quality
ganglionic eminence	UBERON:0004023	93.48	gold quality
rectum	UBERON:0001052	92.17	gold quality
parietal pleura	UBERON:0002400	92.10	gold quality
germinal epithelium of ovary	UBERON:0001304	92.07	gold quality
pleura	UBERON:0000977	91.83	gold quality
mucosa of stomach	UBERON:0001199	91.51	gold quality
visceral pleura	UBERON:0002401	91.28	gold quality
tonsil	UBERON:0002372	90.82	gold quality
ovary	UBERON:0000992	90.68	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.63	gold quality
bone marrow	UBERON:0002371	90.58	gold quality
adrenal tissue	UBERON:0018303	90.40	gold quality
vermiform appendix	UBERON:0001154	90.39	gold quality
esophagus squamous epithelium	UBERON:0006920	90.37	gold quality
subcutaneous adipose tissue	UBERON:0002190	90.34	gold quality
lymph node	UBERON:0000029	90.22	gold quality
right ovary	UBERON:0002118	90.19	gold quality
trabecular bone tissue	UBERON:0002483	90.17	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	90.04	gold quality
bone marrow cell	CL:0002092	90.03	gold quality
right testis	UBERON:0004534	89.95	gold quality
left ovary	UBERON:0002119	89.82	gold quality
endometrium	UBERON:0001295	89.67	gold quality
tibial nerve	UBERON:0001323	89.46	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-6678	yes	7.93
E-ANND-3	yes	6.85
E-GEOD-81383	no	1287.37

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

27 targeting NUP107, 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-548AW	99.99	72.57	3559
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-548AJ-5P	99.78	71.12	3085
HSA-MIR-548F-5P	99.78	71.02	3093
HSA-MIR-548G-5P	99.78	71.12	3085
HSA-MIR-548X-5P	99.78	71.12	3085
HSA-MIR-7154-5P	99.69	70.52	1900
HSA-MIR-4729	99.69	72.18	4233
HSA-MIR-548AV-5P	99.60	70.84	2107
HSA-MIR-548K	99.60	70.84	2107
HSA-MIR-8054	99.48	70.81	2084
HSA-MIR-653-5P	99.46	67.35	1300
HSA-MIR-4666A-5P	99.41	69.72	1887
HSA-MIR-8060	98.61	66.93	1187
HSA-MIR-96-3P	97.47	68.03	839
HSA-MIR-921	97.09	66.45	562
HSA-MIR-597-5P	96.82	67.57	732

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 93.5% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 23)

• Nup107 functions as a keystone Nup that is required for the assembly of a subset of Nups into the nuclear pore complex (PMID:12552102)
• Nup107-160 complex is dynamic in mitosis and that it promotes spindle assembly in a manner that is distinct from its functions at interphase nuclear pores. (PMID:16807356)
• phosphorylation does not affect interactions within the Nup107-160 subcomplex, but regulates the association of the subcomplex with the NPC and other proteins (PMID:17360435)
• These data thus provide the first molecular clues underlying the function of the human Nup107-160 complex at kinetochores. (PMID:17363900)
• When complexed with NUP133, this complex will give the first insights into the protein-protein interactions within a core module of the nuclear pore complex. (PMID:17768364)
• The significant topological differences between Nup107 and Nup133 suggest that helical nucleoporin domains of the nuclear pore complex scaffold fall in different classes and fulfill largely nonredundant functions. (PMID:18570875)
• Data present crystal structures of yNup170(979-1502) and hNup107(658-925) x hNup133(517-1156), and conservation of domain arrangement and of tertiary structure suggests that Nup157/170 and Nup133 derived from a common ancestor. (PMID:19674973)
• A major function of the Nup107 complex in mitosis is to ensure the proper localization of the chromosome passenger complex at the centromere. (PMID:19864462)
• Data show that Nup107-160 promotes spindle assembly through Ran-GTP-regulated nucleation of microtubules by gamma-TuRC at kinetochores, and reveal a relationship between nucleoporins and the microtubule cytoskeleton. (PMID:20081840)
• did a Trypan Blue cell viability assay and it showed increased cell death in NUP107 transfected cells than untreated control (PMID:20490895)
• These findings support the notion that Nup107 may contribute significantly to the regulation of cell fate in aged and transformed cells by modulating nuclear trafficking of signal molecules. (PMID:20833136)
• The SUMO-specific isopeptidase SENP2 associates dynamically with nuclear pore complexes through interactions with karyopherins and the Nup107-160 nucleoporin subcomplex. (PMID:22031293)
• The functions have been ascribed to the NUP107 complex, ranging from Nuclear Pore Complex (NPC) assembly to mRNA export to cell differentiation. (PMID:22713280)
• Study shows that 32 copies of the Nup107 subcomplex assemble into two reticulated rings, one each at the cytoplasmic and nuclear face of the nuclear pore complex. (PMID:24315095)
• The central domain of Nup107 interfered with Apaf-1 nuclear translocation upon genotoxic stress, resulting in a marked reduction of Chk-1 activation and cell cycle arrest. (PMID:25695197)
• Nup107-160 complex and its partner Elys dynamically colocalize with Nup98 and CRM1 into endogenous GLFG bodies present in specific HeLa sublines. (PMID:25904327)
• Biallelic Mutations in Nuclear Pore Complex Subunit NUP107 Cause Early-Childhood-Onset Steroid-Resistant Nephrotic Syndrome. (PMID:26411495)
• a recessive missense mutation in nucleoporin-107 (NUP107, c.1339G>A, p.D447N). This mutation segregated with the XX-GD phenotype and was not present in available databases or in 150 healthy ethnically matched controls. (PMID:26485283)
• Associations between biallelic NUP107 mutations and age at onset in children with steroid-resistant nephrotic syndrome. (PMID:27190346)
• NUP107 was suggested as a candidate in a family with nephrotic syndrome and developmental delay. (PMID:28280135)
• a variant in the 3’-UTR region Nup107 unique to sensitivity to platinum in ovarian cancer, was identified. (PMID:28562428)
• Whole exome sequencing identified a novel and rare missense variant in the NUP107 gene (c.1063C>T, p.R355C) in both sisters with HH. (PMID:29363275)
• Mutations in the NUP93, NUP107 and NUP160 genes cause steroid-resistant nephrotic syndrome in Chinese children. (PMID:38650033)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	nup107	ENSDARG00000016010
mus_musculus	Nup107	ENSMUSG00000052798
rattus_norvegicus	Nup107	ENSRNOG00000006541
drosophila_melanogaster	Nup107	FBGN0027868
caenorhabditis_elegans		WBGENE00003791

Protein

Protein identifiers

Nuclear pore complex protein Nup107 — P57740 (reviewed: P57740)

Alternative names: 107 kDa nucleoporin, Nucleoporin Nup107

All UniProt accessions (4): P57740, F5GY77, G3V1T4, H0YG15

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in the nuclear pore complex (NPC) assembly and/or maintenance. Required for the assembly of peripheral proteins into the NPC. May anchor NUP62 to the NPC. Involved in nephrogenesis.

Subunit / interactions. Part of the nuclear pore complex (NPC). Forms part of the Nup160 subcomplex in the nuclear pore which is composed of NUP160, NUP133, NUP107 and Nup96; this complex plays a role in RNA export and in tethering Nup98 and NUP153 to the nucleus. Does not interact with TPR. Interacts with ZNF106.

Subcellular location. Nucleus membrane. Nucleus. Nuclear pore complex. Chromosome. Centromere. Kinetochore.

Tissue specificity. Ubiquitously expressed in fetal and adult tissues.

Disease relevance. Nephrotic syndrome 11 (NPHS11) [MIM:616730] A form of nephrotic syndrome, a renal disease clinically characterized by severe proteinuria, resulting in complications such as hypoalbuminemia, hyperlipidemia and edema. Kidney biopsies show non-specific histologic changes such as focal segmental glomerulosclerosis and diffuse mesangial proliferation. Some affected individuals have an inherited steroid-resistant form and progress to end-stage renal failure. NPHS11 is an autosomal recessive, steroid-resistant and progressive form with onset in the first decade of life. The disease is caused by variants affecting the gene represented in this entry. Ovarian dysgenesis 6 (ODG6) [MIM:618078] A form of ovarian dysgenesis, a disorder characterized by lack of spontaneous pubertal development, primary amenorrhea, uterine hypoplasia, and hypergonadotropic hypogonadism as a result of streak gonads. ODG6 is an autosomal recessive condition. The disease may be caused by variants affecting the gene represented in this entry. Galloway-Mowat syndrome 7 (GAMOS7) [MIM:618348] A form of Galloway-Mowat syndrome, a severe renal-neurological disease characterized by early-onset nephrotic syndrome associated with microcephaly, central nervous system abnormalities, developmental delays, and a propensity for seizures. Brain anomalies include gyration defects ranging from lissencephaly to pachygyria and polymicrogyria, and cerebellar hypoplasia. Most patients show facial dysmorphism characterized by a small, narrow forehead, large/floppy ears, deep-set eyes, hypertelorism and micrognathia. Additional variable features are visual impairment and arachnodactyly. Most patients die in early childhood. GAMOS7 inheritance is autosomal recessive. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the nucleoporin Nup84/Nup107 family.

Isoforms (3)

UniProt ID	Names	Canonical?
P57740-1	1	yes
P57740-2	2
P57740-3	3

RefSeq proteins (2): NP_001317121, NP_065134* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007252	Nup84/Nup107	Family

Pfam: PF04121

UniProt features (46 total): modified residue 15, helix 12, sequence variant 8, splice variant 3, turn 3, compositionally biased region 2, chain 1, region of interest 1, sequence conflict 1

Structure

Experimental structures (PDB)

7 structures.

PDB	Method	Resolution (Å)
3CQC	X-RAY DIFFRACTION	2.53
3CQG	X-RAY DIFFRACTION	3
3I4R	X-RAY DIFFRACTION	3.53
7R5K	ELECTRON MICROSCOPY	12
5A9Q	ELECTRON MICROSCOPY	23
7PEQ	ELECTRON MICROSCOPY	35
7R5J	ELECTRON MICROSCOPY	50

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P57740-F1	79.99	0.56

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (15): 55, 57, 58, 60, 60, 64, 68, 69, 86, 1, 4, 10, 11, 37, 46

Function

Pathways and Gene Ontology

Reactome pathways

38 pathways

ID	Pathway
R-HSA-1169408	ISG15 antiviral mechanism
R-HSA-141444	Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal
R-HSA-159227	Transport of the SLBP independent Mature mRNA
R-HSA-159230	Transport of the SLBP Dependant Mature mRNA
R-HSA-159231	Transport of Mature mRNA Derived from an Intronless Transcript
R-HSA-159236	Transport of Mature mRNA derived from an Intron-Containing Transcript
R-HSA-165054	Rev-mediated nuclear export of HIV RNA
R-HSA-168271	Transport of Ribonucleoproteins into the Host Nucleus
R-HSA-168276	NS1 Mediated Effects on Host Pathways
R-HSA-168325	Viral Messenger RNA Synthesis
R-HSA-168333	NEP/NS2 Interacts with the Cellular Export Machinery
R-HSA-170822	Regulation of Glucokinase by Glucokinase Regulatory Protein
R-HSA-180746	Nuclear import of Rev protein
R-HSA-180910	Vpr-mediated nuclear import of PICs
R-HSA-1855170	IPs transport between nucleus and cytosol
R-HSA-1855196	IP3 and IP4 transport between cytosol and nucleus
R-HSA-1855229	IP6 and IP7 transport between cytosol and nucleus
R-HSA-191859	snRNP Assembly
R-HSA-2467813	Separation of Sister Chromatids
R-HSA-2500257	Resolution of Sister Chromatid Cohesion
R-HSA-3108214	SUMOylation of DNA damage response and repair proteins
R-HSA-3232142	SUMOylation of ubiquitinylation proteins
R-HSA-3301854	Nuclear Pore Complex (NPC) Disassembly
R-HSA-3371453	Regulation of HSF1-mediated heat shock response
R-HSA-4085377	SUMOylation of SUMOylation proteins
R-HSA-4551638	SUMOylation of chromatin organization proteins
R-HSA-4570464	SUMOylation of RNA binding proteins
R-HSA-4615885	SUMOylation of DNA replication proteins
R-HSA-5619107	Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC)
R-HSA-5663220	RHO GTPases Activate Formins

MSigDB gene sets: 486 (showing top): GOBP_CHROMOSOME_ORGANIZATION, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, REACTOME_INTERACTIONS_OF_VPR_WITH_HOST_CELLULAR_PROTEINS, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM, REACTOME_VIRAL_MESSENGER_RNA_SYNTHESIS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, MODULE_352, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE, MODULE_313, GOBP_NUCLEAR_PORE_ORGANIZATION, GOBP_NUCLEAR_TRANSPORT, WEI_MYCN_TARGETS_WITH_E_BOX, REACTOME_HIV_INFECTION, GOBP_REPRODUCTIVE_SYSTEM_DEVELOPMENT

GO Biological Process (9): post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery (GO:0000973), mRNA export from nucleus (GO:0006406), protein import into nucleus (GO:0006606), nucleocytoplasmic transport (GO:0006913), female gonad development (GO:0008585), nuclear pore complex assembly (GO:0051292), nephron development (GO:0072006), protein transport (GO:0015031), mRNA transport (GO:0051028)

GO Molecular Function (2): structural constituent of nuclear pore (GO:0017056), protein binding (GO:0005515)

GO Cellular Component (11): kinetochore (GO:0000776), nuclear envelope (GO:0005635), nuclear pore (GO:0005643), cytosol (GO:0005829), membrane (GO:0016020), nuclear pore outer ring (GO:0031080), nuclear membrane (GO:0031965), nuclear periphery (GO:0034399), chromosome, centromeric region (GO:0000775), nucleus (GO:0005634), chromosome (GO:0005694)

Reactome top-level categories

Rollup of top-15 pathways:

Category	Pathways
Transport of Mature mRNAs Derived from Intronless Transcripts	3
Inositol phosphate metabolism	3
Interactions of Rev with host cellular proteins	2
Influenza Infection	2
Antimicrobial mechanism of IFN-stimulated genes	1
Amplification of signal from the kinetochores	1
Transport of Mature Transcript to Cytoplasm	1
Late Phase of HIV Life Cycle	1
Influenza Viral RNA Transcription and Replication	1
Export of Viral Ribonucleoproteins from Nucleus	1
Glycolysis	1
Interactions of Vpr with host cellular proteins	1
Metabolism of non-coding RNA	1
Mitotic Anaphase	1
Mitotic Prometaphase	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
nuclear pore	2
intracellular membraneless organelle	2
nucleus	2
nuclear envelope	2
nuclear protein-containing complex	2
transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery	1
RNA export from nucleus	1
gene expression	1
mRNA transport	1
intracellular protein transport	1
protein localization to nucleus	1
import into nucleus	1
establishment of protein localization to organelle	1
nuclear transport	1
gonad development	1
development of primary female sexual characteristics	1
nuclear pore organization	1
pore complex assembly	1
kidney development	1
anatomical structure development	1
transport	1
intracellular protein localization	1
establishment of protein localization	1
RNA transport	1
structural molecule activity	1
nucleocytoplasmic transport	1
binding	1
condensed chromosome, centromeric region	1
supramolecular complex	1
endomembrane system	1
organelle envelope	1
cytoplasm	1
organelle membrane	1
nuclear lumen	1
chromosomal region	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

2983 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
NUP107	NUP160	Q12769	999
NUP107	NUP37	Q8NFH4	999
NUP107	NUP133	Q8WUM0	999
NUP107	SEH1L	Q96EE3	999
NUP107	NUP85	Q9BW27	999
NUP107	NUP98	P52948	998
NUP107	SEC13	P55735	998
NUP107	NUP43	Q8NFH3	996
NUP107	AHCTF1	Q8WYP5	989
NUP107	NUP153	P49790	976
NUP107	NUP205	Q92621	955
NUP107	NUP93	Q8N1F7	943
NUP107	NUP214	P35658	919
NUP107	NUP155	O75694	908
NUP107	NUP62	P37198	901

IntAct

157 interactions, top by confidence:

A	B	Type	Score
NUP133	NUP107	psi-mi:“MI:0915”(physical association)	0.930
NUP107	NUP133	psi-mi:“MI:0915”(physical association)	0.930
NUP107	NUP133	psi-mi:“MI:0914”(association)	0.930
NUP133	NUP98	psi-mi:“MI:0914”(association)	0.730
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
SEC13	SEC16A	psi-mi:“MI:0914”(association)	0.640
NUP43	NUP98	psi-mi:“MI:0914”(association)	0.640
Nup107	NUP98	psi-mi:“MI:0915”(physical association)	0.560
KPNB1	POM121C	psi-mi:“MI:0914”(association)	0.530
FOXP3	FOXP2	psi-mi:“MI:0914”(association)	0.530
NUP43	KIF5B	psi-mi:“MI:0914”(association)	0.530
NUP107	NUP98	psi-mi:“MI:0914”(association)	0.530
NUP98	NUP107	psi-mi:“MI:0914”(association)	0.530
NUP133	NUP153	psi-mi:“MI:0914”(association)	0.530
AHCTF1	NUP98	psi-mi:“MI:0915”(physical association)	0.490
NUP107	GAPDH	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (384): NUP107 (Affinity Capture-MS), NUP107 (Affinity Capture-MS), NUP107 (Affinity Capture-MS), NUP107 (Affinity Capture-MS), NUP107 (Affinity Capture-MS), NUP107 (Affinity Capture-MS), NUP107 (Affinity Capture-MS), NUP107 (Affinity Capture-MS), NUP107 (Co-fractionation), NUP107 (Co-fractionation), NUP107 (Co-fractionation), NUP107 (Co-fractionation), NUP153 (Co-fractionation), NUP37 (Co-fractionation), NUP107 (Affinity Capture-MS)

ESM2 similar proteins: A0JMA8, A1XD93, A1XD94, A1XD95, A1XD97, A4UMC5, A4UMC6, B3DJT0, B5DFC8, E7EXT2, E7F187, F1M3L7, F7AEX0, O14617, O54774, P52590, P53569, P57740, P78344, P79398, Q06AK6, Q0IIX9, Q12929, Q17784, Q17CQ8, Q29RR5, Q2KI89, Q5R4H4, Q5R5K8, Q5R629, Q5R7J9, Q5TYV4, Q5U2Y6, Q5ZII9, Q62448, Q66J74, Q6DI35, Q865S1, Q8BH74, Q8IQ05

Diamond homologs: P52590, P57740, Q8BH74, Q9V466

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
NUP107	“form complex”	NPC	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 161 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Postmitotic nuclear pore complex (NPC) reformation	13	48.6×	1e-17
NEP/NS2 Interacts with the Cellular Export Machinery	14	44.5×	4e-18
Rev-mediated nuclear export of HIV RNA	15	43.6×	5e-19
Nuclear import of Rev protein	14	43.1×	5e-18
Transport of Ribonucleoproteins into the Host Nucleus	13	42.6×	7e-17
IPs transport between nucleus and cytosol	12	41.9×	1e-15
IP3 and IP4 transport between cytosol and nucleus	12	41.9×	1e-15
IP6 and IP7 transport between cytosol and nucleus	12	41.9×	1e-15

GO biological processes:

GO term	Partners	Fold	FDR
RNA export from nucleus	6	41.0×	1e-06
nucleocytoplasmic transport	14	40.0×	2e-16
NLS-bearing protein import into nucleus	6	35.1×	3e-06
mRNA transport	10	19.2×	4e-08
protein import into nucleus	16	16.8×	9e-13
mRNA export from nucleus	6	12.9×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	13
Likely pathogenic	13
Uncertain significance	160
Likely benign	118
Benign	65

Top pathogenic / likely-pathogenic (26)

Variant ID	HGVS	Classification
1942304	NM_020401.4(NUP107):c.262C>T (p.Arg88Ter)	Pathogenic
2082844	NM_020401.4(NUP107):c.178C>T (p.Arg60Ter)	Pathogenic
2104545	NM_020401.4(NUP107):c.1930C>T (p.Arg644Ter)	Pathogenic
219127	NM_020401.4(NUP107):c.2492A>C (p.Asp831Ala)	Pathogenic
219128	NM_020401.4(NUP107):c.1079_1083del (p.Glu360fs)	Pathogenic
219129	NM_020401.4(NUP107):c.969+1G>A	Pathogenic
2426549	NC_000012.11:g.(?69080846)(69096584_?)del	Pathogenic
3635371	NM_020401.4(NUP107):c.1403C>G (p.Ser468Ter)	Pathogenic
3922645	NM_020401.4(NUP107):c.431del (p.Asp144fs)	Pathogenic
4703376	NM_020401.4(NUP107):c.160C>T (p.Arg54Ter)	Pathogenic
4768157	NM_020401.4(NUP107):c.1909A>T (p.Lys637Ter)	Pathogenic
559482	NM_020401.4(NUP107):c.1339G>A (p.Asp447Asn)	Pathogenic
619945	NM_020401.4(NUP107):c.1325G>A (p.Cys442Tyr)	Pathogenic
1685387	NM_020401.4(NUP107):c.2544_2555del (p.Leu848_Leu852delinsPhe)	Likely pathogenic
1687223	NM_020401.4(NUP107):c.580C>T (p.Arg194Ter)	Likely pathogenic
1704953	NM_020401.4(NUP107):c.2101+1G>T	Likely pathogenic
1964591	NM_020401.4(NUP107):c.553-2A>C	Likely pathogenic
219130	NM_020401.4(NUP107):c.469G>T (p.Asp157Tyr)	Likely pathogenic
2630497	NM_020401.4(NUP107):c.1226dup (p.Ser410fs)	Likely pathogenic
2633527	NM_020401.4(NUP107):c.1577-1G>T	Likely pathogenic
2635666	NM_020401.4(NUP107):c.790C>T (p.Arg264Ter)	Likely pathogenic
2788258	NM_020401.4(NUP107):c.303+2T>C	Likely pathogenic
3067843	NM_020401.4(NUP107):c.1063C>T (p.Arg355Cys)	Likely pathogenic
3911747	NM_020401.4(NUP107):c.820G>T (p.Glu274Ter)	Likely pathogenic
4081564	NM_020401.4(NUP107):c.304-45_341dup	Likely pathogenic
590324	NM_020401.4(NUP107):c.2666A>G (p.Tyr889Cys)	Likely pathogenic

SpliceAI

4254 predictions. Top by Δscore:

Variant	Effect	Δscore
12:68689047:GTTT:G	donor_gain	1.0000
12:68689048:TTTT:T	donor_gain	1.0000
12:68689615:GCCTT:G	donor_gain	1.0000
12:68689620:G:GG	donor_gain	1.0000
12:68692061:GAT:G	donor_gain	1.0000
12:68692121:GCAT:G	donor_gain	1.0000
12:68700721:TTCA:T	acceptor_loss	1.0000
12:68700722:TCA:T	acceptor_loss	1.0000
12:68700723:CAG:C	acceptor_loss	1.0000
12:68700724:AGGTG:A	acceptor_loss	1.0000
12:68702785:G:GG	donor_gain	1.0000
12:68709221:A:AG	acceptor_gain	1.0000
12:68709222:A:G	acceptor_gain	1.0000
12:68709224:A:AG	acceptor_gain	1.0000
12:68709225:T:G	acceptor_gain	1.0000
12:68709231:A:AG	acceptor_gain	1.0000
12:68709232:T:G	acceptor_gain	1.0000
12:68709233:AATAG:A	acceptor_gain	1.0000
12:68709236:A:AG	acceptor_gain	1.0000
12:68709236:A:AT	acceptor_loss	1.0000
12:68709237:G:GG	acceptor_gain	1.0000
12:68709237:GGCT:G	acceptor_gain	1.0000
12:68709305:GTCAG:G	donor_gain	1.0000
12:68709306:TCAG:T	donor_loss	1.0000
12:68709307:CAG:C	donor_loss	1.0000
12:68709308:AGG:A	donor_loss	1.0000
12:68709309:GGTAT:G	donor_loss	1.0000
12:68709310:GTATG:G	donor_loss	1.0000
12:68709311:T:A	donor_loss	1.0000
12:68710003:A:AG	acceptor_gain	1.0000

AlphaMissense

6107 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:68700828:T:A	W219R	1.000
12:68700828:T:C	W219R	1.000
12:68719374:T:A	W373R	1.000
12:68719374:T:C	W373R	1.000
12:68710017:T:A	W272R	0.999
12:68710017:T:C	W272R	0.999
12:68715721:G:C	R355P	0.999
12:68715723:G:C	A356P	0.999
12:68719353:T:C	C366R	0.999
12:68719355:T:G	C366W	0.999
12:68719395:G:C	G380R	0.999
12:68719622:T:A	W407R	0.999
12:68719622:T:C	W407R	0.999
12:68721877:T:A	W450R	0.999
12:68721877:T:C	W450R	0.999
12:68735324:T:A	W828R	0.999
12:68735324:T:C	W828R	0.999
12:68700736:T:C	L188P	0.998
12:68700817:A:T	E215V	0.998
12:68700829:G:C	W219S	0.998
12:68700830:G:C	W219C	0.998
12:68700830:G:T	W219C	0.998
12:68713798:T:A	V320D	0.998
12:68715636:G:C	A327P	0.998
12:68715637:C:A	A327D	0.998
12:68715672:G:C	D339H	0.998
12:68715720:C:A	R355S	0.998
12:68719341:G:C	A362P	0.998
12:68719351:T:C	L365P	0.998
12:68719354:G:A	C366Y	0.998

dbSNP variants (sampled 300 via entrez): RS1000027000 (12:68734959 G>A,T), RS1000087583 (12:68687939 G>A), RS1000174719 (12:68703175 G>A), RS1000202838 (12:68708780 A>C), RS1000246108 (12:68694527 G>A), RS1000246817 (12:68731891 A>C), RS1000331184 (12:68739175 A>G), RS1000378509 (12:68738896 C>G,T), RS1000401242 (12:68708871 G>A), RS1000416907 (12:68687463 G>A), RS1000455670 (12:68700457 A>T), RS1000517427 (12:68712218 C>A,T), RS1000581118 (12:68719087 C>T), RS1000608193 (12:68746136 C>G,T), RS1000662045 (12:68721796 C>A,G)

Disease associations

OMIM: gene MIM:607617 | disease phenotypes: MIM:618078, MIM:616730, MIM:618348, MIM:603278

GenCC curated gene-disease

Disease	Classification	Inheritance
nephrotic syndrome, type 11	Strong	Autosomal recessive
ovarian dysgenesis 6	Strong	Autosomal recessive
Galloway-Mowat syndrome 7	Strong	Autosomal recessive
Galloway-Mowat syndrome	Supportive	Autosomal recessive
46 XX gonadal dysgenesis	Supportive	Autosomal dominant
familial idiopathic steroid-resistant nephrotic syndrome	Supportive	Autosomal dominant

Mondo (8): ovarian dysgenesis 6 (MONDO:0054850), nephrotic syndrome, type 11 (MONDO:0014752), Galloway-Mowat syndrome 7 (MONDO:0032692), premature menopause (MONDO:0001119), focal segmental glomerulosclerosis 1 (MONDO:0011303), Galloway-Mowat syndrome (MONDO:0009627), 46 XX gonadal dysgenesis (MONDO:0009299), familial idiopathic steroid-resistant nephrotic syndrome (MONDO:0019006)

Orphanet (2): Hereditary steroid-resistant nephrotic syndrome (Orphanet:656), OBSOLETE: Familial idiopathic steroid-resistant nephrotic syndrome with focal segmental hyalinosis (Orphanet:93213)

HPO phenotypes

97 total (30 of 97 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000013	Hypoplasia of the uterus
HP:0000062	Ambiguous genitalia
HP:0000092	Renal tubular atrophy
HP:0000093	Proteinuria
HP:0000097	Focal segmental glomerulosclerosis
HP:0000100	Nephrotic syndrome
HP:0000112	Nephropathy
HP:0000133	Gonadal dysgenesis
HP:0000144	Decreased fertility
HP:0000164	Abnormality of the dentition
HP:0000175	Cleft palate
HP:0000218	High palate
HP:0000252	Microcephaly
HP:0000316	Hypertelorism
HP:0000319	Smooth philtrum
HP:0000340	Sloping forehead
HP:0000341	Narrow forehead
HP:0000347	Micrognathia
HP:0000365	Hearing impairment
HP:0000400	Macrotia
HP:0000601	Hypotelorism
HP:0000707	Abnormality of the nervous system
HP:0000737	Irritability
HP:0000750	Delayed speech and language development
HP:0000767	Pectus excavatum
HP:0000786	Primary amenorrhea
HP:0000794	IgA deposition in the glomerulus
HP:0000815	Hypergonadotropic hypogonadism
HP:0000823	Delayed puberty

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST000589_1	White blood cell count	3.000000e-08

MeSH disease descriptors (4)

Descriptor	Name	Tree numbers
D023961	Gonadal Dysgenesis, 46,XX	C12.050.351.875.253.064.249; C12.050.351.875.253.309.193; C12.200.706.316.064.249; C12.200.706.316.309.193; C12.800.316.064.249; C12.800.316.309.193; C16.131.939.316.064.249; C16.131.939.316.309.193; C19.391.119.064.249; C19.391.119.309.193
D008594	Menopause, Premature	C12.050.351.500.056.630.250; C12.100.250.056.630.250; G08.686.157.500.500; G08.686.841.249.500.500
C537548	Galloway Mowat syndrome (supp.)
C538457	Segmental glomerulosclerosis (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs79419059	NUP107		0.00	0

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression, decreases expression, increases abundance	2
Resveratrol	affects cotreatment, increases expression	2
Cyclosporine	decreases expression	2
Cadmium Chloride	increases abundance, increases expression, decreases expression	2
FR900359	affects phosphorylation	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
deoxynivalenol	increases expression	1
nobiletin	increases expression, decreases reaction	1
sodium arsenate	decreases reaction, increases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, increases expression	1
cupric chloride	increases expression	1
coumarin	decreases phosphorylation	1
beta-methylcholine	affects expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
2,3-dimethoxy-1,4-naphthoquinone	increases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
ICG 001	decreases expression	1
incobotulinumtoxinA	decreases expression	1
Temozolomide	increases expression	1
Arsenic Trioxide	increases expression	1
Troglitazone	decreases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	increases abundance, increases expression	1
Cadmium	increases abundance, increases expression	1
Calcitriol	decreases expression, affects cotreatment	1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_F1PK	HyCyte HEK293T KO-hNUP107	Transformed cell line	Female

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00417066	PHASE4	COMPLETED	Flexible GnRH Antagonist vs Flare up GnRH Agonist Protocol in Poor Responders
NCT00732693	PHASE4	COMPLETED	Evaluation of Physiologic and Standard Sex Steroid Replacement Regimens in Women With Premature Ovarian Failure
NCT00837616	PHASE4	COMPLETED	Estrogen Dosing in Turner Syndrome: Pharmacology and Metabolism
NCT01853501	PHASE4	UNKNOWN	Effects of ADSC Therapy in Women With POF
NCT02783937	PHASE4	COMPLETED	Filgrastim for Premature Ovarian Insufficiency
NCT03535480	PHASE4	UNKNOWN	Autologous Bone Marrow Stem Cell Ovarian Transplantation to Restore Ovarian Function in Premature Ovarian Failure
NCT00140998	PHASE3	COMPLETED	Estrogen Treatment (Oral vs. Patches) in Turner Syndrome
NCT00001951	PHASE2	COMPLETED	Hormone Replacement in Young Women With Premature Ovarian Failure
NCT00370019	PHASE2	WITHDRAWN	Effects of an Estrogen Replacement Therapy Skin Patch on Ovulation in Women With Premature Ovarian Failure
NCT00429494	PHASE2	COMPLETED	GnRH Analogue for Ovarian Function Preservation in Hematopoietic Stem Cell Transplantation Patients
NCT03816852	PHASE2	SUSPENDED	The Safety and Efficiency Study of Mesenchymal Stem Cell (19#iSCLife®-POI) in Premature Ovarian Insufficiency
NCT04536467	PHASE2	UNKNOWN	Prevention of Chemotherapy-Induced Ovarian Failure With Goserelin in Premenopausal Lymphoma Patients
NCT06117982	PHASE2	COMPLETED	The Impact of Granulocyte Colony Stimulating Factor on Premature Ovarian Insufficiency
NCT02912104	PHASE1	COMPLETED	A Therapeutic Trial of Human Amniotic Epithelial Cells Transplantation for Primary Ovarian Failure
NCT03178695	PHASE1	COMPLETED	Inovium Ovarian Rejuvenation Trials
NCT04815213	PHASE1	ACTIVE_NOT_RECRUITING	The Use of Expandeded Mesenchymal Stromal Cells (MSC) in Premature Ovarian Failure (POF) in Adult Humans
NCT05138367	PHASE1	COMPLETED	Effects of UCA-PSCs in Women With POF
NCT06132542	PHASE1	UNKNOWN	Autologous ADMSC Transplantation in Patients With POI
NCT00948857	PHASE2/PHASE3	TERMINATED	Dehydroepiandrosterone (DHEA) Treatment and Premature Ovarian Failure (POF)
NCT04031456	PHASE2/PHASE3	RECRUITING	Autologous PRP Infusion May Restore Ovarian Function and May Promote Folliculogenesis in POI Patients
NCT02043743	PHASE1/PHASE2	UNKNOWN	Autologous Stem Cells Transplantation in Patients With Idiopathic and Drug Induced Premature Ovarian Failure
NCT02062931	PHASE1/PHASE2	UNKNOWN	Autologous Mesenchymal Stem Cells Transplantation In Women With Premature Ovarian Failure
NCT02151890	PHASE1/PHASE2	COMPLETED	Pregnancy After Stem Cell Transplantation in Premature Ovarian Failure
NCT02372474	PHASE1/PHASE2	COMPLETED	It is a Real The First Baby Of Autologous Stem Cell Therapy in Premature Ovarian Failure
NCT02603744	PHASE1/PHASE2	UNKNOWN	Autologous Adipose Derived Mesenchymal Stromal Cells Transplantation in Women With Premature Ovarian Failure (POF)
NCT02644447	PHASE1/PHASE2	COMPLETED	Transplantation of HUC-MSCs With Injectable Collagen Scaffold for POF
NCT03069209	PHASE1/PHASE2	UNKNOWN	Autologous Bone Marrow-Derived Stem Cell Transplantation in Patients With Premature Ovarian Failure (POF)
NCT03985462	PHASE1/PHASE2	WITHDRAWN	Very Small Embryonic-like Stem Cells for Ovary
NCT04009473	PHASE1/PHASE2	UNKNOWN	Stem Cell Therapy and Growth Factor Ovarian in Vitro Activation
NCT04071574	PHASE1/PHASE2	COMPLETED	Comparative Study on the Efficacy of Ovarian Stimulation Protocols on the Success Rate of ICSI in Female Infertility
NCT04922398	PHASE1/PHASE2	UNKNOWN	Ovarian Injection of PRP (Platelet -Rich Plasma) Vs Normal Saline in Premature Ovarian Insufficiency
NCT05462379	PHASE1/PHASE2	ACTIVE_NOT_RECRUITING	Autologous Heterotopic Fresh Ovarian Graft in Woman With LACC Eligible for Pelvic Radiotherapy Treatment.
NCT06202547	PHASE1/PHASE2	UNKNOWN	Intra-ovarian Injection of MSC-EVs in Idiopathic Premature Ovarian Failure
NCT01129947	EARLY_PHASE1	WITHDRAWN	The Use of DHEA in Women With Premature Ovarian Failure
NCT05522634	EARLY_PHASE1	UNKNOWN	A Clinical Study of Chinese Herbal Compound TJAOA101 in the Treatment of Premature Ovarian Insufficiency
NCT07308327	EARLY_PHASE1	ACTIVE_NOT_RECRUITING	The Influence of Gut Microbiota on Ovarian Function: A Single-center, Randomized,Double Blind, Parallel-controlled, Exploratory Clinical Trial
NCT00001275	Not specified	COMPLETED	Ovarian Follicle Function in Patients With Primary Ovarian Failure
NCT00001306	Not specified	COMPLETED	Steroid Therapy in Autoimmune Premature Ovarian Failure
NCT00006156	Not specified	COMPLETED	Feasibility Study for Development of an Early Test for Ovarian Failure
NCT00119925	Not specified	UNKNOWN	‘SPRING’-Study: Subfertility Guidelines: Patient Related Implementation in the Netherlands Among Gynaecologists