NUP107

nucleoporin 107, the group of Nucleoporins

Basic information

Region (hg38): 12:68686950-68745809

Links

ENSG00000111581 ∙ NCBI:57122 ∙ OMIM:607617 ∙ HGNC:29914 ∙ Uniprot:P57740 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Galloway-Mowat syndrome 7 (Limited), mode of inheritance: AR
• Galloway-Mowat syndrome 7 (Limited), mode of inheritance: AR
• nephrotic syndrome, type 11 (Moderate), mode of inheritance: AR
• ovarian dysgenesis 6 (Limited), mode of inheritance: AR
• 46 XX gonadal dysgenesis (Supportive), mode of inheritance: AD
• Galloway-Mowat syndrome (Supportive), mode of inheritance: AR
• familial idiopathic steroid-resistant nephrotic syndrome (Supportive), mode of inheritance: AD
• Galloway-Mowat syndrome 7 (Strong), mode of inheritance: AR
• nephrotic syndrome, type 11 (Strong), mode of inheritance: AR
• ovarian dysgenesis 6 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Nephrotic syndrome, type 11; Ovarian dysgenesis 6; Galloway-Mowat syndrome 7	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	Craniofacial; Endocrine; Musculoskeletal; Neurologic; Obstetric; Renal	25558065; 26411495; 26485283; 28117080; 28280135; 30179222
In Nephrotic syndrome and Galloway-Mowat syndrome, renal transplantation has been described; In Ovarian dysgenesis, to induce/maintain secondary sex characteristics, specific interventions (eg, medical hormonal treatment) may be necessary

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NUP107 gene.

• not provided (176 variants)
• Inborn genetic diseases (37 variants)
• Nephrotic syndrome, type 11 (9 variants)
• Galloway-Mowat syndrome 7 (4 variants)
• NUP107-related condition (3 variants)
• not specified (2 variants)
• Global developmental delay;Early onset focal segmental glomerulosclerosis;Light complexion (1 variants)
• Nephrotic syndrome, type 11;Ovarian dysgenesis 6;Galloway-Mowat syndrome 7 (1 variants)
• Premature ovarian insufficiency (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUP107 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			2	26	4	32
missense	2	2	62	6		72
nonsense	3	2				5
start loss						0
frameshift		1				1
inframe indel		1	1		1	3
splice donor/acceptor (+/-2bp)		3	1			4
splice region			3	2		5
non coding			1	43	53	97
Total	5	9	67	75	58

Highest pathogenic variant AF is 0.0000329

Variants in NUP107

This is a list of pathogenic ClinVar variants found in the NUP107 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-68687083-G-A		NUP107-related disorder	Likely benign (Jun 15, 2021)
12-68688816-G-A			Benign (Nov 12, 2018)
12-68688870-CT-C			Likely benign (Jan 16, 2020)
12-68688889-A-G			Benign (Aug 20, 2019)
12-68689014-C-T		Premature ovarian insufficiency • Inborn genetic diseases	Uncertain significance (Jun 17, 2022)
12-68689015-G-A		Inborn genetic diseases	Uncertain significance (Dec 19, 2022)
12-68689016-G-T			Likely benign (Feb 16, 2023)
12-68689025-G-A		Galloway-Mowat syndrome 7 • Nephrotic syndrome, type 11	Benign (Jan 31, 2024)
12-68689044-A-G		NUP107-related disorder • Inborn genetic diseases	Benign/Likely benign (Oct 27, 2023)
12-68689457-A-G			Benign (Oct 25, 2019)
12-68689515-T-C			Likely benign (Dec 18, 2023)
12-68689515-T-G			Likely benign (Mar 11, 2022)
12-68689542-C-T		Inborn genetic diseases	Uncertain significance (Feb 17, 2024)
12-68689574-A-G		Inborn genetic diseases	Uncertain significance (Nov 05, 2021)
12-68689593-G-A		Inborn genetic diseases	Uncertain significance (Nov 16, 2023)
12-68689598-C-T		Inborn genetic diseases	Uncertain significance (Jan 26, 2022)
12-68689610-C-T			Pathogenic (Jan 18, 2022)
12-68689632-G-T			Likely benign (Oct 07, 2023)
12-68689638-A-T			Likely benign (Jan 24, 2024)
12-68690346-C-T			Benign (Dec 18, 2019)
12-68690492-A-G			Benign (Jan 16, 2020)
12-68690594-G-T		NUP107-related disorder	Likely benign (Dec 19, 2022)
12-68690618-C-A			Likely benign (Sep 04, 2023)
12-68690638-A-G			Likely benign (Sep 01, 2022)
12-68690646-G-A		Inborn genetic diseases	Uncertain significance (Dec 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUP107	protein_coding	protein_coding	ENST00000229179	28	56272

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.56e-9	1.00	125659	0	88	125747	0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.89	373	490	0.760	0.0000257	6080
Missense in Polyphen		122	171.01	0.71341		2203
Synonymous	0.913	149	164	0.909	0.00000823	1681
Loss of Function	4.34	26	63.3	0.411	0.00000348	714

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000394	0.000391
Ashkenazi Jewish	0.00	0.00
East Asian	0.000631	0.000598
Finnish	0.000278	0.000277
European (Non-Finnish)	0.000427	0.000404
Middle Eastern	0.000631	0.000598
South Asian	0.000544	0.000490
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the nuclear pore complex (NPC) assembly and/or maintenance (PubMed:12552102, PubMed:15229283). Required for the assembly of peripheral proteins into the NPC (PubMed:15229283, PubMed:12552102). May anchor NUP62 to the NPC (PubMed:15229283). {ECO:0000269|PubMed:12552102, ECO:0000269|PubMed:15229283}.
• Pathway: RNA transport - Homo sapiens (human);Gastric Cancer Network 1;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: 0.155

Intolerance Scores

• loftool: 0.177
• rvis_EVS: -0.55
• rvis_percentile_EVS: 19.86

Haploinsufficiency Scores

• pHI: 0.910
• hipred: Y
• hipred_score: 0.694
• ghis: 0.657

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.992

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nup107
• Phenotype: reproductive system phenotype

Zebrafish Information Network

• Gene name: nup107
• Affected structure: glomerular capillary
• Phenotype tag: abnormal
• Phenotype quality: collapsed

Gene ontology

• Biological process: posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery;mRNA export from nucleus;protein import into nucleus;female gonad development;viral process;nuclear pore complex assembly
• Cellular component: kinetochore;condensed chromosome kinetochore;nuclear envelope;nuclear pore;cytosol;membrane;nuclear pore outer ring;nuclear membrane;nuclear periphery
• Molecular function: protein binding;structural constituent of nuclear pore