NUP133

nucleoporin 133, the group of Minor histocompatibility antigens|Nucleoporins

Basic information

Region (hg38): 1:229440259-229508341

Links

ENSG00000069248 ∙ NCBI:55746 ∙ OMIM:607613 ∙ HGNC:18016 ∙ Uniprot:Q8WUM0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Galloway-Mowat syndrome 8 (Strong), mode of inheritance: AR
• Galloway-Mowat syndrome 8 (Limited), mode of inheritance: AR
• Galloway-Mowat syndrome (Supportive), mode of inheritance: AR
• familial idiopathic steroid-resistant nephrotic syndrome (Supportive), mode of inheritance: AD
• Galloway-Mowat syndrome 8 (Limited), mode of inheritance: Unknown
• nephrotic syndrome, type 18 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Nephrotic syndrome, type 18; Galloway-Mowat syndrome 8	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	Audiologic/Otolaryngologic; Craniofacial; Neurologic; Renal	11793129; 30179222; 30427554
In Galloway-Mowat syndrome, renal transplantation has been described

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NUP133 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUP133 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	48	7	56
missense		2	113	7	8	130
nonsense		1	1			2
start loss						0
frameshift		1	1			2
inframe indel			1			1
splice donor/acceptor (+/-2bp)			1			1
splice region			2	8	1	11
non coding				16	4	20
Total	0	4	118	71	19

Variants in NUP133

This is a list of pathogenic ClinVar variants found in the NUP133 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-229441926-T-C			Uncertain significance (Mar 21, 2022)
1-229441943-C-G			Uncertain significance (-)
1-229441955-G-A		NUP133-related disorder	Likely benign (Oct 20, 2023)
1-229441965-T-C		not specified	Uncertain significance (Nov 21, 2023)
1-229441970-C-A		not specified	Uncertain significance (May 08, 2023)
1-229441971-T-G			Uncertain significance (May 06, 2022)
1-229441976-G-A			Likely benign (Sep 05, 2023)
1-229441977-C-A		not specified	Uncertain significance (Nov 08, 2022)
1-229441991-C-T		NUP133-related disorder	Benign (May 23, 2023)
1-229441992-G-T			Uncertain significance (Sep 27, 2023)
1-229442012-C-T			Likely benign (Apr 23, 2023)
1-229442015-C-T			Likely benign (Dec 16, 2023)
1-229442016-G-A		Nephrotic syndrome, type 18 • not specified	Uncertain significance (Jun 05, 2024)
1-229442044-T-C			Likely benign (Jul 27, 2022)
1-229442051-A-T		Galloway-Mowat syndrome 8	Pathogenic (Jul 18, 2022)
1-229442058-A-C			Likely benign (Dec 30, 2023)
1-229444913-C-A			Likely pathogenic (May 27, 2022)
1-229444939-C-T			Likely benign (Feb 04, 2022)
1-229444949-A-G		Nephrotic syndrome, type 18	Uncertain significance (Jun 03, 2020)
1-229444994-C-T		not specified	Uncertain significance (Nov 17, 2023)
1-229449164-T-C			Benign (Jan 25, 2024)
1-229449166-G-C			Uncertain significance (Mar 21, 2022)
1-229449197-A-G		NUP133-related disorder	Likely benign (Apr 02, 2022)
1-229450516-T-G			Likely benign (Nov 30, 2022)
1-229450530-C-T			Uncertain significance (Oct 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUP133	protein_coding	protein_coding	ENST00000261396	26	67059

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000926	1.00	125650	0	97	125747	0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	526	596	0.882	0.0000301	7518
Missense in Polyphen		243	308.77	0.787		3991
Synonymous	-0.486	230	221	1.04	0.0000112	2226
Loss of Function	5.17	20	64.9	0.308	0.00000350	772

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00304	0.00303
Ashkenazi Jewish	0.00	0.00
East Asian	0.000331	0.000326
Finnish	0.000279	0.000277
European (Non-Finnish)	0.000196	0.000185
Middle Eastern	0.000331	0.000326
South Asian	0.0000327	0.0000327
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in poly(A)+ RNA transport. {ECO:0000269|PubMed:11684705}.
• Pathway: RNA transport - Homo sapiens (human);tRNA processing;Disease;Signal Transduction;Gene expression (Transcription);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;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;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;RHO GTPases Activate Formins;Pyrimidine metabolism;SUMOylation;Glycosphingolipid metabolism;Cellular responses to external stimuli;Regulation of Glucokinase by Glucokinase Regulatory Protein;Glycolysis;RHO GTPase Effectors;Phosphatidylinositol phosphate metabolism;Signaling by Rho GTPases;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;Metabolism of non-coding RNA;Cellular response to heat stress;Nuclear Envelope Breakdown;Mitotic Prophase;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Nuclear import of Rev protein;Glucose metabolism;Transcriptional regulation by small RNAs;Cell Cycle;Resolution of Sister Chromatid Cohesion;Interactions of Vpr with host cellular proteins;Glycine, serine, alanine and threonine metabolism;Cell Cycle, Mitotic;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA;Arachidonic acid metabolism;Gene Silencing by RNA (Consensus)

Recessive Scores

• pRec: 0.248

Intolerance Scores

• loftool: 0.711
• rvis_EVS: 0.52
• rvis_percentile_EVS: 80.36

Haploinsufficiency Scores

• pHI: 0.523
• hipred: Y
• hipred_score: 0.516
• ghis: 0.603

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.941

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nup133
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); growth/size/body region 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); homeostasis/metabolism phenotype

Gene ontology

• Biological process: mRNA export from nucleus;protein import into nucleus;nuclear pore organization;viral process;neural tube development;neurogenesis;nuclear pore distribution;paraxial mesoderm development;somite development
• Cellular component: condensed chromosome kinetochore;condensed chromosome outer kinetochore;nuclear envelope;nuclear pore;cytosol;membrane;nuclear pore outer ring;nuclear membrane
• Molecular function: protein binding;structural constituent of nuclear pore