NUP210L

nucleoporin 210 like, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 1:153992689-154155116

Links

ENSG00000143552 ∙ NCBI:91181 ∙ ∙ HGNC:29915 ∙ Uniprot:Q5VU65 ∙ 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 NUP210L gene.

• Inborn genetic diseases (47 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUP210L 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			46	1		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	2	0

Variants in NUP210L

This is a list of pathogenic ClinVar variants found in the NUP210L region.

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

Position	Type	Phenotype	Significance	ClinVar
1-153992870-G-A		not specified	Uncertain significance (Mar 20, 2023)
1-153992871-A-T		not specified	Uncertain significance (Jan 23, 2023)
1-153992935-C-T		not specified	Uncertain significance (Mar 29, 2022)
1-153995151-G-A		not specified	Uncertain significance (May 24, 2023)
1-154000907-T-G		not specified	Uncertain significance (Apr 27, 2022)
1-154000927-T-C		not specified	Uncertain significance (Nov 17, 2022)
1-154000946-C-A		not specified	Uncertain significance (Nov 07, 2022)
1-154000969-T-C		not specified	Uncertain significance (Aug 30, 2021)
1-154001017-T-C		not specified	Likely benign (Dec 15, 2023)
1-154001018-G-T		not specified	Uncertain significance (Sep 06, 2022)
1-154001036-C-T		not specified	Uncertain significance (Jul 27, 2022)
1-154001832-G-A		not specified	Uncertain significance (Sep 01, 2021)
1-154001958-C-A		not specified	Uncertain significance (Mar 07, 2023)
1-154009983-C-G		not specified	Uncertain significance (Jan 24, 2024)
1-154010060-C-T		not specified	Uncertain significance (May 27, 2022)
1-154018976-A-G		not specified	Likely benign (Feb 05, 2024)
1-154019012-G-C		not specified	Uncertain significance (Jul 06, 2021)
1-154022272-A-G		not specified	Uncertain significance (Oct 26, 2021)
1-154023181-A-G			Likely benign (Jun 01, 2022)
1-154023201-T-C		not specified	Uncertain significance (Oct 03, 2022)
1-154023233-G-T		not specified	Uncertain significance (Aug 08, 2022)
1-154025630-T-G		not specified	Uncertain significance (Nov 01, 2022)
1-154025700-C-T		not specified	Uncertain significance (Aug 09, 2021)
1-154027573-A-T		not specified	Uncertain significance (Nov 21, 2022)
1-154029954-C-G		not specified	Uncertain significance (Feb 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUP210L	protein_coding	protein_coding	ENST00000368559	40	162432

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000320	1.00	124718	0	81	124799	0.000325

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.68	774	1.01e+3	0.764	0.0000514	12345
Missense in Polyphen		127	259.11	0.49014		3285
Synonymous	0.768	351	370	0.949	0.0000186	3796
Loss of Function	6.54	26	94.7	0.275	0.00000521	1085

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000850	0.000844
Ashkenazi Jewish	0.00	0.00
East Asian	0.000446	0.000445
Finnish	0.00	0.00
European (Non-Finnish)	0.000426	0.000415
Middle Eastern	0.000446	0.000445
South Asian	0.000230	0.000229
Other	0.000167	0.000165

dbNSFP

Source: dbNSFP

• Pathway: RNA transport - Homo sapiens (human);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: 0.0766

Intolerance Scores

• loftool: 0.773
• rvis_EVS: -0.65
• rvis_percentile_EVS: 16.14

Haploinsufficiency Scores

• pHI: 0.0897
• hipred: N
• hipred_score: 0.471

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.122

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nup210l
• Phenotype: reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: spermatid development;Sertoli cell development
• Cellular component: nuclear pore;integral component of membrane