NUP160
protein-codingnucleoporin 160, the group of Nucleoporins
Gene summary
A structural constituent of nuclear pore. Involved in mRNA export from nucleus and nephron development. Located in kinetochore and nuclear envelope. Part of nuclear pore outer ring. Implicated in nephrotic syndrome type 19. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~70.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0032582
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0019006
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0032582
Submitter: ClinGen
*NUP160* was first reported in relation to autosomal recessive nephrotic syndrome 19 in 2018 (Braun et al., PMID: 30179222). Nephrotic syndrome 19 is characterized as a disease of renal glomerular filter, featuring proteinuria, edema, and hypoalbuminemia. It does not respond to drug treatment and inevitably progresses to end-stage renal disease, thus requiring dialysis or renal transplantation for survival. Renal histology shows focal segmental glomerulosclerosis. 5 variants (missense, in-frame indel, nonsense,) that have been reported in 3 probands in 3 publications (PMIDs: 30179222, 30910934,38650033) are included in this curation. The mechanism of pathogenicity is unclear. This gene-disease relationship is also supported by a fly rescue model and knockout mouse models (PMIDs: 30910934, 38224683). This gene-disease pair was originally evaluated by the Glomerulopathy GCEP on Feburary 12, 2023. It was re-evaluated on July 23, 2024. As a result of this reevaluation, the classification increased from Limited to Moderate with the addition of a new individual case and mouse model (PMIDs: 38650033, 38224683).
Inheritance Pattern: AR
Disease ID:MONDO:0032582
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0032582
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Renal
Intervention: General
Rationale: 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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NUP160 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015231.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 59 | 5 | 67 | ||
| missense | 260 | 15 | 3 | 278 | ||
| nonsense | 2 | 2 | 2 | 6 | ||
| start loss | 0 | |||||
| frameshift | 2 | 1 | 3 | |||
| splice donor/acceptor (+/-2bp) | 1 | 6 | 7 | |||
| Total | 4 | 3 | 272 | 74 | 8 | 361 |
Highest pathogenic variant AF is 0.000006571684
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056046.2 | 36 | MANE Select | |
| Ensembl | ENSP00000367721.3 | 36 | MANE Select | |
| RefSeq | NP_001305328.1 | 3 | Standard | |
| Ensembl | ENSP00000431495.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- RNA transport - Homo sapiens (human)
- tRNA processing
- Disease
- Signal Transduction
- Gene expression (Transcription)
Biological Process
- mRNA export from nucleus
- viral process
Molecular Function
- protein binding
- structural constituent of nuclear pore
Cellular Component
- kinetochore
- nuclear envelope
- nuclear pore
- cytosol
- nuclear pore outer ring
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000378460
- Coding exons
- 36
- Length
- 70469
- Individuals with no LoFs
- 125647
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 101
- Defined
- 125748
- p
- 0.000402
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.04 | 698 | 780 | 0.895 | 0.0000405 | 9336 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.00038 | 0.00038 | rare |
| Ashkenazi Jewish | 0.0019 | 0.0019 | notable |
| East Asian | 0.00027 | 0.00027 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00034 | 0.00033 | rare |
| South Asian | 0.00056 | 0.00056 | rare |
| Other | 0.00018 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in poly(A)+ RNA transport. {ECO:0000269|PubMed:11684705}.;
Recessive Scores
- pRec
- 0.121
Intolerance Scores
- LoFtool
- 0.918
- RVIS EVS
- -1.77
- RVIS percentile EVS
- 2.32
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.912
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |