NUP37

nucleoporin 37, the group of WD repeat domain containing|Nucleoporins

Basic information

Region (hg38): 12:102073102-102120120

Links

ENSG00000075188 ∙ NCBI:79023 ∙ OMIM:609264 ∙ HGNC:29929 ∙ Uniprot:Q8NFH4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• familial idiopathic steroid-resistant nephrotic syndrome (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Microcephaly 24, primary, autosomal recessive	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	Musculoskeletal; Neurologic	30179222

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NUP37 gene.

• Inborn genetic diseases (9 variants)
• Microcephaly 24, primary, autosomal recessive (4 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUP37 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		1
missense			10			10
nonsense		1				1
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region						0
non coding						0
Total	2	1	10	1	0

Highest pathogenic variant AF is 0.00000657

Variants in NUP37

This is a list of pathogenic ClinVar variants found in the NUP37 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-102074387-G-T		not specified	Uncertain significance (Mar 29, 2022)
12-102074391-C-T		not specified	Uncertain significance (Jun 24, 2022)
12-102074415-G-A		not specified	Uncertain significance (Jan 18, 2023)
12-102074418-C-T		not specified	Uncertain significance (Feb 05, 2024)
12-102074419-G-A		Microcephaly 24, primary, autosomal recessive	Likely pathogenic (Jan 10, 2019)
12-102076830-C-A			Uncertain significance (-)
12-102076854-G-T		NUP37-related disorder	Benign (Dec 18, 2019)
12-102077365-C-T		NUP37-related disorder	Likely benign (Apr 18, 2019)
12-102077443-T-C		not specified	Uncertain significance (May 03, 2023)
12-102085803-C-A		not specified	Uncertain significance (Sep 26, 2022)
12-102085809-G-C		not specified	Uncertain significance (Aug 16, 2021)
12-102099119-C-T		Microcephaly 24, primary, autosomal recessive	Uncertain significance (Dec 16, 2019)
12-102101071-T-C		NUP37-related disorder	Benign (Oct 30, 2019)
12-102112163-C-CA		Microcephaly 24, primary, autosomal recessive	Pathogenic (Jan 16, 2020)
12-102112177-T-C		not specified	Uncertain significance (Apr 27, 2022)
12-102118354-T-C		NUP37-related disorder	Benign (May 28, 2019)
12-102118356-G-T		NUP37-related disorder	Likely benign (Mar 27, 2019)
12-102118359-TAACCTGA-T		Microcephaly 24, primary, autosomal recessive	Pathogenic (May 04, 2022)
12-102118369-C-T		NUP37-related disorder	Likely benign (Aug 01, 2022)
12-102118370-G-A		not specified	Uncertain significance (Aug 12, 2021)
12-102118371-T-C		not specified	Uncertain significance (Oct 20, 2023)
12-102118382-A-G		not specified	Uncertain significance (Feb 07, 2023)
12-102118391-T-C		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUP37	protein_coding	protein_coding	ENST00000552283	9	45936

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000108	0.947	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.470	152	169	0.898	0.00000822	2138
Missense in Polyphen		38	43.703	0.86951		538
Synonymous	1.10	49	59.8	0.820	0.00000321	600
Loss of Function	1.80	11	19.6	0.561	0.00000102	232

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000526	0.000525
Ashkenazi Jewish	0.00	0.00
East Asian	0.000119	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000810	0.0000791
Middle Eastern	0.000119	0.000109
South Asian	0.000178	0.000163
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the Nup107-160 subcomplex of the nuclear pore complex (NPC). The Nup107-160 subcomplex is required for the assembly of a functional NPC. The Nup107-160 subcomplex is also required for normal kinetochore microtubule attachment, mitotic progression and chromosome segregation. {ECO:0000269|PubMed:17363900}.
• 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: 0.130

Intolerance Scores

• loftool: 0.665
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

• pHI: 0.948
• hipred: Y
• hipred_score: 0.765
• ghis: 0.731

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.871

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nup37

Zebrafish Information Network

• Gene name: nup37
• Affected structure: atrium
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: mRNA export from nucleus;cell cycle;chromosome segregation;viral process;cell division
• Cellular component: kinetochore;condensed chromosome kinetochore;nucleus;nuclear envelope;nucleoplasm;cytosol;nuclear pore outer ring
• Molecular function: protein binding