NYNRIN

protein-coding

NYN domain and retroviral integrase containing

Gene summary

Predicted to enable RNA endonuclease activity and mRNA binding activity. Predicted to be involved in 3'-UTR-mediated mRNA destabilization. Predicted to be located in membrane. Predicted to be active in cytoplasmic ribonucleoprotein granule and nucleus. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

KIAA1305

MANE transcript

NM_025081.3

Inheritance

ClinVar variants

U:388B:127

Top phenotype

Predisposition to Wilms tumor

gnomAD constraint

pLI —, LoF o/e 0.41

Max pathogenic AF

—

Genomic locus

chr14:24,399,003-24,419,283

External References & Databases

Ensembl (ENSG00000205978)

Transcript & Mutation Effects

hg38 • Region Span ~20.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

hereditary Wilms tumorMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0003321

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NYNRIN variants in ClinVar

6 Conditions Cataloged

not providedTotal: 311

not specifiedTotal: 257

Predisposition to Wilms tumorTotal: 30

NYNRIN-related disorderTotal: 22

Wilms Tumor PredispositionTotal: 3

HepatoblastomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_025081.3. 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			27 clinvar	93 clinvar	5 clinvar	125
missense			351 clinvar	24 clinvar	5 clinvar	380
nonsense			3 clinvar			3
start loss						0
frameshift			5 clinvar			5
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	388	117	10	515

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_025081.3	RefSeq	NP_079357.2	8	MANE Select
ENST00000382554.4	Ensembl	ENSP00000371994.3	8	MANE Select
ENST00000938047.1	Ensembl	ENSP00000608106.1	8	Standard
ENST00001133259.1	Ensembl	ENSP00000811326.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process
DNA integration

Molecular Function

molecular_function
nucleic acid binding

Cellular Component

cellular_component
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000382554
Coding exons: 8
Length: 20503
Individuals with no LoFs: 124903
Homozygous LoFs: 0
Heterozygous LoFs: 70
Defined: 124973
p: 0.000280

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.57	911	1.05e+3	0.864	0.0000585	12184
Missense (PolyPhen)		292	407.18	0.71713		4714
Synonymous	-0.337	470	461	1.02	0.0000267	4080
Loss of Function	4.47	27	66.3	0.408	0.00000353	674

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00046	0.00044	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.00019	0.00019	rare
European (Non-Finnish)	0.00035	0.00034	rare
South Asian	0.00016	0.00016	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0970

Intolerance Scores

LoFtool: 0.688
RVIS EVS: -1.01
RVIS percentile EVS: 8.22

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.231

Gene Damage Prediction

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