NUP160

nucleoporin 160, the group of Nucleoporins

Basic information

Region (hg38): 11:47778086-47848555

Links

ENSG00000030066 ∙ NCBI:23279 ∙ OMIM:607614 ∙ HGNC:18017 ∙ Uniprot:Q12769 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• nephrotic syndrome, type 19 (Strong), mode of inheritance: AR
• familial idiopathic steroid-resistant nephrotic syndrome (Supportive), mode of inheritance: AD
• nephrotic syndrome, type 19 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Nephrotic syndrome, type 19	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	30179222

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NUP160 gene.

• not provided (131 variants)
• Inborn genetic diseases (69 variants)
• Nephrotic syndrome, type 19 (7 variants)
• NUP160-related condition (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUP160 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			3	13	9	25
missense			119	8	3	130
nonsense	1		1			2
start loss						0
frameshift	2					2
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			4	3	3	10
non coding				17	9	26
Total	3	0	124	38	21

Highest pathogenic variant AF is 0.000112

Variants in NUP160

This is a list of pathogenic ClinVar variants found in the NUP160 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-47779146-C-G			Uncertain significance (May 25, 2022)
11-47779150-T-G		not specified	Uncertain significance (Dec 14, 2023)
11-47779164-CCT-C		Nephrotic syndrome, type 19	Pathogenic (-)
11-47779171-T-C		NUP160-related disorder	Benign (Jan 25, 2024)
11-47779197-A-G		NUP160-related disorder	Conflicting classifications of pathogenicity (May 19, 2022)
11-47780327-GA-G			Likely benign (Jun 13, 2023)
11-47780345-C-T		not specified	Uncertain significance (Apr 28, 2022)
11-47780379-A-G			Likely benign (Jul 15, 2022)
11-47780382-T-C			Likely benign (Aug 24, 2023)
11-47780399-T-C		not specified	Uncertain significance (Jan 24, 2024)
11-47780401-G-A		not specified	Uncertain significance (Aug 08, 2023)
11-47780406-G-A		NUP160-related disorder	Benign/Likely benign (Jan 15, 2024)
11-47780409-T-C			Likely benign (Apr 30, 2023)
11-47780423-T-C		not specified	Uncertain significance (Oct 29, 2021)
11-47780426-G-C			Uncertain significance (Jul 21, 2022)
11-47783059-T-C			Likely benign (Sep 10, 2023)
11-47783064-T-TATAC			Likely benign (Oct 21, 2022)
11-47783075-C-T			Uncertain significance (Oct 17, 2022)
11-47783113-T-C			Uncertain significance (Jun 13, 2022)
11-47783141-C-T		not specified	Uncertain significance (Dec 14, 2023)
11-47783161-T-G		not specified	Uncertain significance (Dec 21, 2021)
11-47783179-A-C			Uncertain significance (Dec 01, 2023)
11-47783212-G-A			Likely benign (Dec 20, 2023)
11-47784915-C-G			Likely benign (Dec 25, 2023)
11-47784916-G-A			Uncertain significance (Aug 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUP160	protein_coding	protein_coding	ENST00000378460	36	70469

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000678	1.00	125647	0	101	125748	0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	698	780	0.895	0.0000405	9336
Missense in Polyphen		146	198.49	0.73555		2397
Synonymous	0.213	274	279	0.984	0.0000135	2764
Loss of Function	6.08	27	88.8	0.304	0.00000475	1033

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000686	0.000686
Ashkenazi Jewish	0.00190	0.00189
East Asian	0.000275	0.000272
Finnish	0.000144	0.000139
European (Non-Finnish)	0.000338	0.000334
Middle Eastern	0.000275	0.000272
South Asian	0.000564	0.000555
Other	0.000178	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in poly(A)+ RNA transport. {ECO:0000269|PubMed:11684705}.
• Pathway: RNA transport - Homo sapiens (human);tRNA processing;Disease;Signal Transduction;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;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;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;RHO GTPases Activate Formins;Pyrimidine metabolism;SUMOylation;Glycosphingolipid metabolism;Cellular responses to external stimuli;Regulation of Glucokinase by Glucokinase Regulatory Protein;Glycolysis;RHO GTPase Effectors;Phosphatidylinositol phosphate metabolism;Signaling by Rho GTPases;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;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Nuclear import of Rev protein;Glucose metabolism;Transcriptional regulation by small RNAs;Cell Cycle;Resolution of Sister Chromatid Cohesion;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: 0.121

Intolerance Scores

• loftool: 0.918
• rvis_EVS: -1.77
• rvis_percentile_EVS: 2.32

Haploinsufficiency Scores

• pHI: 0.870
• hipred: Y
• hipred_score: 0.655
• ghis: 0.688

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.912

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nup160

Gene ontology

• Biological process: mRNA export from nucleus;viral process
• Cellular component: kinetochore;nuclear envelope;nuclear pore;cytosol;nuclear pore outer ring
• Molecular function: protein binding;structural constituent of nuclear pore