NUP210L

protein-coding

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

Gene summary

Predicted to act upstream of or within Sertoli cell development and spermatid development. Predicted to be located in nuclear membrane. Predicted to be part of nuclear pore. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_207308.3

Inheritance

ClinVar variants

P:1U:186B:12

Top phenotype

Spermatogenic failure 97

gnomAD constraint

pLI —, LoF o/e 0.27

Max pathogenic AF

—

Genomic locus

chr1:153,992,690-154,155,116

External References & Databases

Ensembl (ENSG00000143552)

Transcript & Mutation Effects

hg38 • Region Span ~162.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

spermatogenic failureLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0004983

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Spermatogenic failure 97AR

Manifestation: Genitourinary

Intervention: General

Rationale: 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

Refs: 33332558

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NUP210L variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 190

Spermatogenic failure 97Total: 2

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_207308.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar		3
missense			181 clinvar	10 clinvar		191
nonsense			2 clinvar			2
start loss						0
frameshift		1 clinvar				1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	1	186	12	0	199

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_207308.3	RefSeq	NP_997191.2	40	MANE Select
ENST00000368559.8	Ensembl	ENSP00000357547.3	40	MANE Select
NM_001159484.1	RefSeq	NP_001152956.1	38	Standard
ENST00000271854.3	Ensembl	ENSP00000271854.3	38	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

RNA transport - Homo sapiens (human)
Glycolysis and Gluconeogenesis
Leukotriene metabolism
Squalene and cholesterol biosynthesis
Purine metabolism

Biological Process

spermatid development
Sertoli cell development

Cellular Component

nuclear pore
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368559
Coding exons: 40
Length: 162432
Individuals with no LoFs: 124718
Homozygous LoFs: 0
Heterozygous LoFs: 81
Defined: 124799
p: 0.000325

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.68	774	1.01e+3	0.764	0.0000514	12345
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00059	0.00058	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00045	0.00045	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00043	0.00041	rare
South Asian	0.00023	0.00023	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0766

Intolerance Scores

LoFtool: 0.773
RVIS EVS: -0.65
RVIS percentile EVS: 16.14

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.122

Gene Damage Prediction

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