NUP188

nucleoporin 188, the group of Armadillo like helical domain containing|Nucleoporins

Basic information

Region (hg38): 9:128947699-129007096

Previous symbols: [ "KIAA0169" ]

Links

ENSG00000095319 ∙ NCBI:23511 ∙ OMIM:615587 ∙ HGNC:17859 ∙ Uniprot:Q5SRE5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• sandestig-stefanova syndrome (Moderate), mode of inheritance: AR
• sandestig-stefanova syndrome (Strong), mode of inheritance: AR
• sandestig-stefanova syndrome (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Sandestig-Stefanova syndrome	AR	Cardiovascular	The condition can involve congenital cardiac anomalies, and awareness may allow early management	Cardiovascular; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic	32021605; 32275884

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NUP188 gene.

• not provided (2 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUP188 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				22	5	27
missense			177	16	1	194
nonsense	2	1	1			4
start loss						0
frameshift	1	3				4
inframe indel			1			1
splice donor/acceptor (+/-2bp)		2	1			3
splice region			3		3	6
non coding			1	3	6	10
Total	3	6	181	41	12

Variants in NUP188

This is a list of pathogenic ClinVar variants found in the NUP188 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-128947707-C-T		DK1-congenital disorder of glycosylation	Benign/Likely benign (Jun 16, 2018)
9-128947714-G-A		DK1-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
9-128947727-C-T		DK1-congenital disorder of glycosylation • Inborn genetic diseases	Uncertain significance (Dec 21, 2023)
9-128947736-G-C		Inborn genetic diseases • NUP188-related disorder	Likely benign (Jan 07, 2022)
9-128947738-G-A		Congenital disorder of glycosylation	Benign/Likely benign (Jun 28, 2018)
9-128947744-T-G		Inborn genetic diseases	Uncertain significance (Nov 17, 2022)
9-128947745-G-A		Inborn genetic diseases	Uncertain significance (Dec 30, 2023)
9-128947846-A-G			Benign (Jun 19, 2018)
9-128947888-G-A			Benign (Jul 09, 2018)
9-128947907-A-G			Likely benign (Jun 16, 2018)
9-128948062-C-T			Benign (Jun 29, 2018)
9-128949197-G-A		Inborn genetic diseases	Uncertain significance (Jul 09, 2024)
9-128949218-T-C		Inborn genetic diseases	Uncertain significance (Nov 08, 2022)
9-128949243-G-A		Inborn genetic diseases	Conflicting classifications of pathogenicity (Jun 04, 2021)
9-128952806-C-T		Inborn genetic diseases	Uncertain significance (Dec 18, 2023)
9-128952809-C-T			Pathogenic (Feb 01, 2023)
9-128956360-G-C		Inborn genetic diseases	Uncertain significance (Jan 10, 2023)
9-128956361-C-G		Inborn genetic diseases	Uncertain significance (Jul 07, 2024)
9-128956378-A-G		Inborn genetic diseases • NUP188-related disorder	Likely benign (Dec 01, 2024)
9-128956978-G-T		Inborn genetic diseases	Uncertain significance (May 02, 2024)
9-128956991-T-TA		Sandestig-stefanova syndrome	Uncertain significance (Oct 01, 2019)
9-128958019-C-T		Sandestig-stefanova syndrome	Likely pathogenic (Dec 01, 2018)
9-128958855-C-T			Likely benign (Dec 31, 2019)
9-128958875-A-G		Inborn genetic diseases	Uncertain significance (Jun 24, 2022)
9-128958885-C-T		NUP188-related disorder	Benign (Nov 11, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUP188	protein_coding	protein_coding	ENST00000372577	44	59398

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.954	0.0457	125624	1	123	125748	0.000493

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	881	980	0.899	0.0000559	11343
Missense in Polyphen		313	397.13	0.78816		4695
Synonymous	-0.731	398	380	1.05	0.0000207	3503
Loss of Function	7.29	20	97.9	0.204	0.00000483	1133

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00145	0.00145
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.000218	0.000217
Finnish	0.000141	0.000139
European (Non-Finnish)	0.000468	0.000466
Middle Eastern	0.000218	0.000217
South Asian	0.000859	0.000817
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as a component of the nuclear pore complex (NPC).
• Disease: DISEASE: Note=Copy number variations of NUP188 gene may be a cause of heterotaxy, a congenital heart disease resulting from abnormalities in left-right (LR) body patterning. {ECO:0000269|PubMed:21282601}.
• 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: 0.126

Intolerance Scores

• loftool: 0.710
• rvis_EVS: -1.25
• rvis_percentile_EVS: 5.37

Haploinsufficiency Scores

• pHI: 0.663
• hipred: N
• hipred_score: 0.250
• ghis: 0.597

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.842

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nup188

Gene ontology

• Biological process: mRNA export from nucleus;protein import into nucleus;viral process;glomerular visceral epithelial cell migration
• Cellular component: nuclear envelope;membrane;nuclear pore inner ring
• Molecular function: structural constituent of nuclear pore