NUP93

nucleoporin 93, the group of Nucleoporins

Basic information

Region (hg38): 16:56730117-56850286

Links

ENSG00000102900 ∙ NCBI:9688 ∙ OMIM:614351 ∙ HGNC:28958 ∙ Uniprot:Q8N1F7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• nephrotic syndrome, type 12 (Moderate), mode of inheritance: AR
• familial idiopathic steroid-resistant nephrotic syndrome (Supportive), mode of inheritance: AD
• nephrotic syndrome, type 12 (Strong), mode of inheritance: AR
• nephrotic syndrome, type 12 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Nephrotic syndrome, type 12	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Renal	26878725

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NUP93 gene.

• not provided (2 variants)
• Nephrotic syndrome, type 12 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUP93 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	41	10	52
missense		1	71	9	1	82
nonsense	1					1
start loss						0
frameshift	1	1				2
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1	3				4
splice region			1	8	2	11
non coding				39	30	69
Total	3	5	73	89	41

Variants in NUP93

This is a list of pathogenic ClinVar variants found in the NUP93 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-56747918-C-T			Benign (Nov 12, 2018)
16-56748233-G-A		Nephrotic syndrome, type 12	Likely pathogenic (Jul 05, 2023)
16-56748329-C-A			Uncertain significance (Dec 11, 2023)
16-56748364-G-A		NUP93-related disorder	Benign (Dec 26, 2023)
16-56748377-C-T		Inborn genetic diseases	Uncertain significance (Aug 17, 2022)
16-56748383-C-T		Inborn genetic diseases	Uncertain significance (Oct 06, 2021)
16-56748400-G-A			Benign (Dec 27, 2023)
16-56748411-C-T		Inborn genetic diseases	Uncertain significance (Jun 18, 2021)
16-56748427-G-A			Likely pathogenic (Oct 14, 2022)
16-56748435-T-G		Nephrotic syndrome, type 12	Benign/Likely benign (Dec 26, 2023)
16-56758448-C-G			Benign (May 20, 2021)
16-56758527-T-A		Nephrotic syndrome, type 12	Benign (Jan 29, 2024)
16-56758550-C-T			Likely benign (Jun 08, 2022)
16-56758557-C-T		Inborn genetic diseases	Uncertain significance (May 15, 2024)
16-56758568-C-T			Likely benign (May 08, 2023)
16-56758569-A-G			Likely benign (Jan 25, 2024)
16-56758587-C-T			Pathogenic (Jul 05, 2022)
16-56758608-G-A		Inborn genetic diseases	Uncertain significance (May 08, 2024)
16-56758610-C-T			Likely benign (Jan 29, 2024)
16-56758639-A-G		Inborn genetic diseases	Uncertain significance (Apr 27, 2022)
16-56758652-T-G		Inborn genetic diseases	Uncertain significance (May 09, 2024)
16-56798381-T-C			Likely benign (Jul 26, 2020)
16-56798390-C-T			Benign (Nov 12, 2018)
16-56798464-C-A			Likely benign (Aug 04, 2023)
16-56798484-G-A		NUP93-related disorder	Benign/Likely benign (Jan 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUP93	protein_coding	protein_coding	ENST00000308159	21	114781

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000175	1.00	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	409	490	0.835	0.0000298	5375
Missense in Polyphen		115	151.7	0.7581		1763
Synonymous	-0.934	208	192	1.09	0.0000119	1575
Loss of Function	4.05	19	49.9	0.381	0.00000289	527

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000786	0.000725
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000600	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.0000600	0.0000544
South Asian	0.0000657	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the nuclear pore complex (NPC) assembly and/or maintenance (PubMed:9348540). May anchor nucleoporins, but not NUP153 and TPR, to the NPC. During renal development, regulates podocyte migration and proliferation through SMAD4 signaling (PubMed:26878725). {ECO:0000269|PubMed:15229283, ECO:0000269|PubMed:15703211, ECO:0000269|PubMed:26878725, ECO:0000269|PubMed:9348540}.
• Disease: DISEASE: Nephrotic syndrome 12 (NPHS12) [MIM:616892]: 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. NPHS12 inheritance is autosomal recessive. {ECO:0000269|PubMed:26878725}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: RNA transport - Homo sapiens (human);tRNA processing;Disease;Gene expression (Transcription);Regulation of HSF1-mediated heat shock response;Metabolism of carbohydrates;Rev-mediated nuclear export of HIV RNA;Late Phase of HIV Life Cycle;HIV Life Cycle;Interactions of Rev with host cellular proteins;Host Interactions of HIV factors;HIV Infection;snRNP Assembly;Vpr-mediated nuclear import of PICs;SUMOylation of DNA damage response and repair proteins;Transport of Ribonucleoproteins into the Host Nucleus;Viral Messenger RNA Synthesis;Export of Viral Ribonucleoproteins from Nucleus;SUMOylation of chromatin organization proteins;Influenza Viral RNA Transcription and Replication;Cellular responses to stress;SUMOylation of RNA binding proteins;Post-translational protein modification;SUMOylation of DNA replication proteins;SUMO E3 ligases SUMOylate target proteins;NEP/NS2 Interacts with the Cellular Export Machinery;Metabolism of proteins;Influenza Life Cycle;Influenza Infection;Metabolism of RNA;Glycolysis and Gluconeogenesis;Infectious disease;Leukotriene metabolism;Squalene and cholesterol biosynthesis;Purine metabolism;Vitamin B3 (nicotinate and nicotinamide) metabolism;Vitamin B5 - CoA biosynthesis from pantothenate;Metabolism;Transport of the SLBP independent Mature mRNA;Transport of the SLBP Dependant Mature mRNA;Transport of Mature mRNA Derived from an Intronless Transcript;Transport of Mature mRNAs Derived from Intronless Transcripts;Pyrimidine metabolism;SUMOylation;Glycosphingolipid metabolism;Cellular responses to external stimuli;Regulation of Glucokinase by Glucokinase Regulatory Protein;Glycolysis;Phosphatidylinositol phosphate metabolism;Lysine metabolism;Methionine and cysteine metabolism;Selenoamino acid metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Aminosugars metabolism;Pentose phosphate pathway;Nuclear Pore Complex (NPC) Disassembly;De novo fatty acid biosynthesis;Glycerophospholipid metabolism;Prostaglandin formation from dihomo gama-linoleic acid;Putative anti-Inflammatory metabolites formation from EPA;Vitamin D3 (cholecalciferol) metabolism;Vitamin E metabolism;tRNA processing in the nucleus;Transport of Mature mRNA derived from an Intron-Containing Transcript;Metabolism of non-coding RNA;Cellular response to heat stress;Nuclear Envelope Breakdown;Mitotic Prophase;M Phase;Nuclear import of Rev protein;Glucose metabolism;Transcriptional regulation by small RNAs;Cell Cycle;Interactions of Vpr with host cellular proteins;Glycine, serine, alanine and threonine metabolism;Cell Cycle, Mitotic;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA;Arachidonic acid metabolism;Gene Silencing by RNA (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.678
• rvis_EVS: -1.41
• rvis_percentile_EVS: 4.13

Haploinsufficiency Scores

• pHI: 0.981
• hipred: Y
• hipred_score: 0.706
• ghis: 0.643

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.969

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nup93

Zebrafish Information Network

• Gene name: nup93
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: mRNA export from nucleus;protein import into nucleus;nuclear envelope organization;viral process;poly(A)+ mRNA export from nucleus;nuclear pore complex assembly;positive regulation of SMAD protein signal transduction;SMAD protein signal transduction;renal system development;glomerular visceral epithelial cell development;glomerular visceral epithelial cell migration;negative regulation of hydrogen peroxide-induced cell death
• Cellular component: nuclear envelope;nuclear pore;membrane;nuclear membrane;nuclear periphery
• Molecular function: protein binding;structural constituent of nuclear pore