NUP205

nucleoporin 205, the group of Nucleoporins|Armadillo like helical domain containing

Basic information

Region (hg38): 7:135557916-135648757

Previous symbols: [ "C7orf14" ]

Links

ENSG00000155561 ∙ NCBI:23165 ∙ OMIM:614352 ∙ HGNC:18658 ∙ Uniprot:Q92621 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• familial idiopathic steroid-resistant nephrotic syndrome (Supportive), mode of inheritance: AD
• nephrotic syndrome, type 13 (Strong), mode of inheritance: AR
• nephrotic syndrome, type 13 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Nephrotic syndrome, type 13	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	Renal	26878725
Renal transplantation has been described

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NUP205 gene.

• not provided (318 variants)
• Inborn genetic diseases (65 variants)
• Nephrotic syndrome, type 13 (13 variants)
• Marfanoid habitus and intellectual disability (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUP205 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				55	15	70
missense		1	125	8	6	140
nonsense			2			2
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			7	10	3	20
non coding			2	52	96	150
Total	0	1	130	115	117

Variants in NUP205

This is a list of pathogenic ClinVar variants found in the NUP205 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-135557940-C-T			Benign (Jul 28, 2020)
7-135557949-C-G			Uncertain significance (Nov 27, 2023)
7-135557955-C-T		NUP205-related disorder	Benign (Jan 09, 2024)
7-135557969-T-A		not specified	Uncertain significance (Aug 30, 2022)
7-135557986-G-C			Likely benign (Jul 21, 2023)
7-135557999-T-C			Likely benign (Dec 29, 2019)
7-135558162-C-T			Benign (Nov 12, 2018)
7-135558225-T-G			Benign (Nov 12, 2018)
7-135558264-A-G			Likely benign (Apr 20, 2020)
7-135570839-T-A			Benign (Jan 19, 2021)
7-135570857-T-TATATAA			Likely benign (Feb 03, 2020)
7-135570871-A-ATATATGTAATATATTATATATTATATATT			Benign (Dec 18, 2019)
7-135570950-A-ATAGT			Benign (Dec 08, 2020)
7-135571078-G-A			Benign (Feb 03, 2020)
7-135571113-C-G		not specified	Uncertain significance (Apr 14, 2022)
7-135571133-C-T			Likely benign (Oct 10, 2023)
7-135571151-A-G			Likely benign (Mar 14, 2023)
7-135571188-C-T			Uncertain significance (Sep 29, 2022)
7-135571229-C-T		NUP205-related disorder	Likely benign (Nov 13, 2023)
7-135571246-C-T			Uncertain significance (Nov 27, 2023)
7-135571279-AT-A			Benign (Jul 14, 2020)
7-135571298-C-T			Benign (Feb 03, 2020)
7-135571306-G-C			Likely benign (Feb 03, 2020)
7-135571368-C-A			Likely benign (Feb 03, 2020)
7-135571411-TA-T			Benign (Apr 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUP205	protein_coding	protein_coding	ENST00000285968	43	90839

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000310	125717	0	31	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.35	955	1.08e+3	0.884	0.0000578	13096
Missense in Polyphen		284	349.38	0.81288		4343
Synonymous	-0.442	393	382	1.03	0.0000191	3912
Loss of Function	8.37	18	115	0.157	0.00000616	1321

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000427	0.000425
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the nuclear pore complex (NPC) assembly and/or maintenance (PubMed:9348540). May anchor NUP62 and other nucleoporins, but not NUP153 and TPR, to the NPC (PubMed:15229283). {ECO:0000269|PubMed:15229283, ECO:0000269|PubMed:9348540}.
• Disease: DISEASE: Nephrotic syndrome 13 (NPHS13) [MIM:616893]: A form of nephrotic syndrome, a renal disease clinically characterized by severe proteinuria, resulting in complications such as hypoalbuminemia, hyperlipidemia and edema. Kidney biopsies show non-specific histologic changes such as focal segmental glomerulosclerosis and diffuse mesangial proliferation. Some affected individuals have an inherited steroid-resistant form and progress to end-stage renal failure. {ECO:0000269|PubMed:26878725}. 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);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;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;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA;Arachidonic acid metabolism;Gene Silencing by RNA (Consensus)

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.502
• rvis_EVS: -0.96
• rvis_percentile_EVS: 9.01

Haploinsufficiency Scores

• pHI: 0.971
• hipred: Y
• hipred_score: 0.637
• ghis: 0.662

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.898

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nup205

Zebrafish Information Network

• Gene name: nup205
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: curved dorsal

Gene ontology

• Biological process: mRNA export from nucleus;nucleocytoplasmic transport;nuclear pore organization;viral process;nuclear pore complex assembly
• Cellular component: nuclear envelope;nuclear pore;membrane;nuclear membrane;nuclear periphery;nuclear pore inner ring
• Molecular function: protein binding;structural constituent of nuclear pore