NUP62
nucleoporin 62, the group of Nucleoporins
Basic information
Region (hg38): 19:49906825-49929764
Links
Phenotypes
GenCC
Source:
- familial infantile bilateral striatal necrosis (Strong), mode of inheritance: AR
- familial infantile bilateral striatal necrosis (Limited), mode of inheritance: AR
- familial infantile bilateral striatal necrosis (Supportive), mode of inheritance: AD
- familial infantile bilateral striatal necrosis (Limited), mode of inheritance: Unknown
- Leigh syndrome (Disputed Evidence), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Striatonigral degeneration, infantile | 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 | Neurologic | 3729745; 12374138; 14718703; 16786527 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (175 variants)
- not_specified (82 variants)
- NUP62-related_disorder (12 variants)
- Familial_infantile_bilateral_striatal_necrosis (4 variants)
- Infantile_bilateral_striatal_necrosis (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUP62 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016553.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 58 | 66 | ||||
| missense | 131 | 143 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 0 | 132 | 66 | 11 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NUP62 | protein_coding | protein_coding | ENST00000596217 | 1 | 22939 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.950 | 0.0498 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.00622 | 304 | 304 | 0.999 | 0.0000197 | 3318 |
| Missense in Polyphen | 49 | 54.971 | 0.89138 | 743 | ||
| Synonymous | -1.37 | 164 | 143 | 1.15 | 0.0000113 | 1194 |
| Loss of Function | 2.85 | 0 | 9.43 | 0.00 | 4.23e-7 | 116 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Essential component of the nuclear pore complex (PubMed:1915414). The N-terminal is probably involved in nucleocytoplasmic transport (PubMed:1915414). The C-terminal is involved in protein-protein interaction probably via coiled-coil formation, promotes its association with centrosomes and may function in anchorage of p62 to the pore complex (PubMed:1915414, PubMed:24107630). Plays a role in mitotic cell cycle progression by regulating centrosome segregation, centriole maturation and spindle orientation (PubMed:24107630). It might be involved in protein recruitment to the centrosome after nuclear breakdown (PubMed:24107630). {ECO:0000269|PubMed:1915414, ECO:0000269|PubMed:24107630}.;
- Disease
- DISEASE: Infantile striatonigral degeneration (SNDI) [MIM:271930]: Neurological disorder characterized by symmetrical degeneration of the caudate nucleus, putamen, and occasionally the globus pallidus, with little involvement of the rest of the brain. The clinical features include developmental regression, choreoathetosis, dystonia, spasticity, dysphagia, failure to thrive, nystagmus, optic atrophy, and mental retardation. {ECO:0000269|PubMed:16786527}. 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);sumoylation by ranbp2 regulates transcriptional repression;cycling of ran in nucleocytoplasmic transport;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;mechanism of protein import into the nucleus;Signaling events mediated by HDAC Class II;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;Sumoylation by RanBP2 regulates transcriptional repression;Transport of Mature Transcript to Cytoplasm;Signaling events mediated by HDAC Class I;Processing of Capped Intron-Containing Pre-mRNA;Arachidonic acid metabolism;Gene Silencing by RNA
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- -0.53
- rvis_percentile_EVS
- 20.86
Haploinsufficiency Scores
- pHI
- 0.721
- hipred
- Y
- hipred_score
- 0.664
- ghis
- 0.453
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.988
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nup62
- Phenotype
- mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- transcription, DNA-templated;mRNA export from nucleus;protein import into nucleus;mitotic metaphase plate congression;centrosome cycle;mitotic centrosome separation;cell surface receptor signaling pathway;spermatogenesis;cell aging;cell death;negative regulation of cell population proliferation;hormone-mediated signaling pathway;regulation of signal transduction;viral process;negative regulation of epidermal growth factor receptor signaling pathway;regulation of protein import into nucleus;negative regulation of apoptotic process;negative regulation of programmed cell death;positive regulation of I-kappaB kinase/NF-kappaB signaling;negative regulation of MAP kinase activity;positive regulation of epidermal growth factor receptor signaling pathway;positive regulation of mitotic nuclear division;positive regulation of transcription, DNA-templated;regulation of Ras protein signal transduction;negative regulation of Ras protein signal transduction;positive regulation of centriole replication;regulation of mitotic spindle organization;protein heterotrimerization;centriole assembly;positive regulation of mitotic cytokinetic process;positive regulation of protein localization to centrosome
- Cellular component
- spindle pole;nucleus;nuclear envelope;annulate lamellae;nuclear pore;cytoplasm;centrosome;nuclear membrane;nuclear pore central transport channel;mitotic spindle;Flemming body;ribonucleoprotein complex
- Molecular function
- chromatin binding;protein binding;phospholipid binding;structural constituent of nuclear pore;kinesin binding;receptor signaling complex scaffold activity;Hsp70 protein binding;SH2 domain binding;ubiquitin binding;thyroid hormone receptor binding;PTB domain binding;Hsp90 protein binding