NUP62CL

nucleoporin 62 C-terminal like

Basic information

Region (hg38): X:107123426-107206433

Links

ENSG00000198088 ∙ NCBI:54830 ∙ ∙ HGNC:25960 ∙ Uniprot:Q9H1M0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NUP62CL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUP62CL 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	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	2	0

Variants in NUP62CL

This is a list of pathogenic ClinVar variants found in the NUP62CL region.

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

Position	Type	Phenotype	Significance	ClinVar
X-107153217-C-G		not specified	Uncertain significance (Jan 18, 2022)
X-107153227-G-A		not specified	Uncertain significance (Jul 19, 2022)
X-107153229-G-A		not specified	Likely benign (May 01, 2022)
X-107153499-C-T		not specified	Uncertain significance (Nov 27, 2023)
X-107154124-T-C		not specified	Uncertain significance (Jul 06, 2021)
X-107154191-A-G		not specified	Uncertain significance (Oct 27, 2022)
X-107154209-C-T		not specified	Uncertain significance (Apr 06, 2024)
X-107154222-T-C			Likely benign (Aug 01, 2022)
X-107167685-C-T		not specified	Uncertain significance (Dec 16, 2023)
X-107167739-G-A		not specified	Uncertain significance (Mar 25, 2024)
X-107167740-T-C		not specified	Uncertain significance (Sep 23, 2023)
X-107167773-T-C		not specified	Uncertain significance (Mar 21, 2022)
X-107175121-G-T		not specified	Uncertain significance (Aug 21, 2023)
X-107175128-A-G		not specified	Uncertain significance (Sep 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUP62CL	protein_coding	protein_coding	ENST00000372466	6	83014

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00131	0.666	125638	4	1	125643	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.268	54	59.8	0.902	0.00000409	1175
Missense in Polyphen		8	9.6879	0.82577		244
Synonymous	0.783	19	23.9	0.796	0.00000172	354
Loss of Function	0.679	5	6.93	0.721	4.37e-7	137

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000727	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000123	0.00000880
Middle Eastern	0.0000727	0.0000544
South Asian	0.000185	0.0000982
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Glycolysis and Gluconeogenesis;Leukotriene metabolism;Squalene and cholesterol biosynthesis;Purine metabolism;Vitamin B3 (nicotinate and nicotinamide) metabolism;Vitamin B5 - CoA biosynthesis from pantothenate;Pyrimidine metabolism;Glycosphingolipid metabolism;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;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;Glycine, serine, alanine and threonine metabolism;Arachidonic acid metabolism (Consensus)

Recessive Scores

• pRec: 0.0646

Intolerance Scores

• loftool: 0.687
• rvis_EVS: 0.81
• rvis_percentile_EVS: 87.82

Haploinsufficiency Scores

• pHI: 0.0621
• hipred: N
• hipred_score: 0.123
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.273

Mouse Genome Informatics

• Gene name: Nup62cl

Gene ontology

• Biological process: nucleocytoplasmic transport;protein transport
• Cellular component: nuclear pore
• Molecular function: protein binding;structural constituent of nuclear pore