NUP210
protein-codingnucleoporin 210, the group of Nucleoporins
Gene summary
The nuclear pore complex is a massive structure that extends across the nuclear envelope, forming a gateway that regulates the flow of macromolecules between the nucleus and the cytoplasm. Nucleoporins are the main components of the nuclear pore complex in eukaryotic cells. The protein encoded by this gene is a membrane-spanning glycoprotein that is a major component of the nuclear pore complex. Multiple pseudogenes related to this gene are located on chromosome 3. [provided by RefSeq, Jul 2013]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~104.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: Unknown
Disease ID:MONDO:0005090
Submitter: Labcorp Genetics (formerly Invitae)
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NUP210 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024923.4. 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 | 4 | 8 | 1 | 13 | ||
| missense | 315 | 27 | 2 | 344 | ||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 10 | 10 | ||||
| Total | 0 | 0 | 331 | 35 | 3 | 369 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_079199.2 | 40 | MANE Select | |
| Ensembl | ENSP00000254508.5 | 40 | MANE Select | |
| Ensembl | ENSP00000511960.1 | 16 | Standard | |
| Ensembl | ENSP00000587009.1 | 40 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| nup210 | Danio rerio | Structure: muscle cell Quality: undulate abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- RNA transport - Homo sapiens (human)
- tRNA processing
- Disease
- Gene expression (Transcription)
- sumoylation by ranbp2 regulates transcriptional repression
Biological Process
- mRNA export from nucleus
- viral process
Molecular Function
- protein dimerization activity
Cellular Component
- nuclear envelope
- nuclear pore
- endoplasmic reticulum membrane
- membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000254508
- Coding exons
- 40
- Length
- 104073
- Individuals with no LoFs
- 125564
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 183
- Defined
- 125748
- p
- 0.000732
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.782 | 1070 | 1.14e+3 | 0.935 | 0.0000710 | 12161 |
| Missense (PolyPhen) | 176 | 222.94 | 0.78945 | 2447 | ||
| Synonymous | -0.955 | 532 | 505 | 1.05 | 0.0000361 | 3966 |
| Loss of Function | 3.66 | 50 | 86.8 | 0.576 | 0.00000431 | 945 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00062 | 0.00062 | rare |
| Latino/Admixed American | 0.00064 | 0.00064 | rare |
| Ashkenazi Jewish | 0.00080 | 0.00079 | rare |
| East Asian | 0.00044 | 0.00038 | rare |
| Finnish | 0.000048 | 0.000046 | rare |
| European (Non-Finnish) | 0.00076 | 0.00076 | rare |
| South Asian | 0.0014 | 0.0013 | notable |
| Other | 0.0015 | 0.0015 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Nucleoporin essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as structural integrity. {ECO:0000269|PubMed:14517331}.;
Recessive Scores
- pRec
- 0.139
Intolerance Scores
- LoFtool
- 0.793
- RVIS EVS
- -2.01
- RVIS percentile EVS
- 1.72
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.785
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |