NUP210

nucleoporin 210, the group of Nucleoporins

Basic information

Region (hg38): 3:13316235-13420322

Links

ENSG00000132182 ∙ NCBI:23225 ∙ OMIM:607703 ∙ HGNC:30052 ∙ Uniprot:Q8TEM1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NUP210 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUP210 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				6	1	7
missense			125	18	2	145
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					2	2
Total	0	0	125	24	5

Variants in NUP210

This is a list of pathogenic ClinVar variants found in the NUP210 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-13316486-A-G			Benign (Apr 29, 2020)
3-13317697-G-T		not specified	Uncertain significance (Apr 18, 2024)
3-13317721-G-A		not specified	Uncertain significance (Oct 22, 2021)
3-13317754-G-A		not specified	Uncertain significance (Feb 22, 2023)
3-13317769-G-A		not specified	Uncertain significance (May 16, 2023)
3-13319092-C-T		not specified	Uncertain significance (Dec 22, 2023)
3-13319116-G-A		not specified	Uncertain significance (Jul 12, 2023)
3-13319131-C-T		not specified	Conflicting classifications of pathogenicity (Sep 26, 2023)
3-13319244-G-A		not specified	Uncertain significance (Oct 05, 2021)
3-13319271-G-A		not specified	Uncertain significance (Jan 02, 2024)
3-13319781-G-A		not specified	Uncertain significance (Mar 23, 2022)
3-13319940-C-T		not specified	Uncertain significance (Aug 16, 2022)
3-13319946-C-T		not specified	Uncertain significance (Oct 04, 2022)
3-13321602-C-T		NUP210-related disorder	Likely benign (Jul 28, 2022)
3-13321607-G-A		not specified	Uncertain significance (Oct 25, 2022)
3-13321672-G-A			Benign (Jul 10, 2018)
3-13321707-C-G		not specified	Uncertain significance (Apr 29, 2024)
3-13321736-G-C		not specified	Uncertain significance (Mar 13, 2023)
3-13321787-C-T		not specified	Uncertain significance (Apr 25, 2022)
3-13321818-T-C		not specified	Likely benign (Mar 29, 2023)
3-13321821-A-C		not specified	Uncertain significance (Jun 28, 2022)
3-13322283-T-C		not specified	Uncertain significance (Jan 10, 2023)
3-13322315-T-C		not specified	Uncertain significance (Jan 02, 2024)
3-13323393-G-A		not specified	Uncertain significance (Aug 23, 2021)
3-13325815-G-A		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUP210	protein_coding	protein_coding	ENST00000254508	40	104073

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.10e-22	1.00	125564	1	183	125748	0.000732

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.782	1070	1.14e+3	0.935	0.0000710	12161
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00126	0.00126
Ashkenazi Jewish	0.000803	0.000794
East Asian	0.000441	0.000381
Finnish	0.0000475	0.0000462
European (Non-Finnish)	0.000761	0.000756
Middle Eastern	0.000441	0.000381
South Asian	0.00138	0.00134
Other	0.00148	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Nucleoporin essential for nuclear pore assembly and fusion, nuclear pore spacing, as well as structural integrity. {ECO:0000269|PubMed:14517331}.
• 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)

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.793
• rvis_EVS: -2.01
• rvis_percentile_EVS: 1.72

Haploinsufficiency Scores

• pHI: 0.167
• hipred: N
• hipred_score: 0.481
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.785

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nup210

Zebrafish Information Network

• Gene name: nup210
• Affected structure: muscle cell
• Phenotype tag: abnormal
• Phenotype quality: undulate

Gene ontology

• Biological process: mRNA export from nucleus;viral process
• Cellular component: nuclear envelope;nuclear pore;endoplasmic reticulum membrane;membrane;integral component of membrane;nuclear membrane
• Molecular function: protein dimerization activity