NUP210L

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

Basic information

Region (hg38): 1:153992690-154155116

Links

ENSG00000143552 ∙ NCBI:91181 ∙ ∙ HGNC:29915 ∙ Uniprot:Q5VU65 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 97	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	Genitourinary	33332558

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NUP210L gene.

• not_specified (166 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. These statistics are base on transcript: NM_000207308.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			157	8		165
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	157	10	0

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