NUP62

nucleoporin 62, the group of Nucleoporins

Basic information

Region (hg38): 19:49906824-49929764

Links

ENSG00000213024 ∙ NCBI:23636 ∙ OMIM:605815 ∙ HGNC:8066 ∙ Uniprot:P37198 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• 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: CGD

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 ClinVar and linked to the NUP62 gene.

• not provided (134 variants)
• Inborn genetic diseases (24 variants)
• not specified (8 variants)
• Infantile bilateral striatal necrosis (5 variants)
• Familial infantile bilateral striatal necrosis (1 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.

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	37	11	49
missense			77	4	4	85
nonsense						0
start loss						0
frameshift			1			1
inframe indel			10		1	11
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	89	41	16

Variants in NUP62

This is a list of pathogenic ClinVar variants found in the NUP62 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-49908261-C-G			Uncertain significance (Aug 16, 2022)
19-49908264-C-T			Uncertain significance (Oct 06, 2023)
19-49908283-G-A			Uncertain significance (Oct 13, 2023)
19-49908288-T-A		not specified	Uncertain significance (Nov 02, 2023)
19-49908290-G-A			Benign (Jan 29, 2024)
19-49908305-C-G		not specified	Uncertain significance (Sep 26, 2023)
19-49908325-G-A			Benign (Jan 06, 2024)
19-49908326-C-G			Likely benign (Sep 13, 2017)
19-49908363-A-T		not specified	Uncertain significance (May 11, 2022)
19-49908364-T-A		not specified	Uncertain significance (May 04, 2023)
19-49908372-T-C			Uncertain significance (Apr 11, 2023)
19-49908396-A-G		not specified	Uncertain significance (Oct 05, 2023)
19-49908403-C-CA			Uncertain significance (Aug 13, 2022)
19-49908413-G-A			Likely benign (Jul 25, 2023)
19-49908420-G-A			Uncertain significance (Apr 06, 2022)
19-49908421-C-T			Uncertain significance (Aug 03, 2023)
19-49908425-G-A			Likely benign (Jan 18, 2024)
19-49908442-C-T		not specified	Uncertain significance (Dec 20, 2023)
19-49908451-C-T			Uncertain significance (Dec 02, 2021)
19-49908470-G-A		NUP62-related disorder	Benign (Aug 04, 2023)
19-49908485-A-G		not specified • Infantile bilateral striatal necrosis	Benign (Feb 01, 2024)
19-49908487-C-T			Uncertain significance (Sep 30, 2022)
19-49908520-G-A			Uncertain significance (Jan 13, 2022)
19-49908529-C-T		not specified	Uncertain significance (Nov 03, 2023)
19-49908549-G-A		not specified	Uncertain significance (Jan 22, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

• 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