NRDE2

NRDE-2, necessary for RNA interference, domain containing

Basic information

Region (hg38): 14:90267859-90331969

Previous symbols: [ "C14orf102" ]

Links

ENSG00000119720 ∙ NCBI:55051 ∙ OMIM:618631 ∙ HGNC:20186 ∙ Uniprot:Q9H7Z3 ∙ 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 NRDE2 gene.

• Inborn genetic diseases (59 variants)
• not provided (4 variants)
• Neurodevelopmental disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NRDE2 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				2		2
missense			55	3	1	59
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	58	5	1

Variants in NRDE2

This is a list of pathogenic ClinVar variants found in the NRDE2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-90268235-T-A		not specified	Uncertain significance (Jun 27, 2022)
14-90269498-T-C		Neurodevelopmental disorder with poor growth, spastic tetraplegia, and hearing loss	Pathogenic (Jun 09, 2023)
14-90270221-T-C		not specified	Uncertain significance (Sep 16, 2021)
14-90278380-C-A		not specified	Uncertain significance (Aug 15, 2023)
14-90278386-G-A		not specified	Uncertain significance (Sep 22, 2023)
14-90278428-C-T		not specified	Uncertain significance (Sep 27, 2021)
14-90278432-G-T		not specified	Uncertain significance (Oct 13, 2021)
14-90278443-C-T		not specified	Uncertain significance (Jun 29, 2022)
14-90278446-C-T		not specified	Uncertain significance (Aug 30, 2021)
14-90279129-G-A		not specified	Uncertain significance (Aug 09, 2021)
14-90286385-G-T		not specified	Uncertain significance (Oct 16, 2023)
14-90286404-C-T		not specified	Uncertain significance (Oct 20, 2023)
14-90286456-C-G		not specified	Uncertain significance (Jun 28, 2022)
14-90288305-T-C		not specified	Likely benign (Jan 10, 2023)
14-90288314-A-G		not specified	Uncertain significance (Mar 29, 2023)
14-90288367-G-T		not specified	Uncertain significance (Sep 27, 2021)
14-90288412-G-A		not specified	Uncertain significance (Oct 12, 2021)
14-90288424-C-T		not specified	Uncertain significance (Mar 07, 2024)
14-90288496-G-C		not specified	Uncertain significance (Dec 14, 2021)
14-90288542-C-G		not specified	Uncertain significance (May 18, 2023)
14-90288542-C-T		not specified	Uncertain significance (Jul 19, 2023)
14-90288574-A-G		not specified	Uncertain significance (Sep 29, 2022)
14-90288593-C-T			Benign (Sep 11, 2018)
14-90288631-T-C		not specified	Uncertain significance (Aug 10, 2021)
14-90288671-G-A			Likely benign (Nov 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NRDE2	protein_coding	protein_coding	ENST00000354366	14	55902

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.80e-15	0.998	125459	0	289	125748	0.00115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.168	631	643	0.981	0.0000347	7686
Missense in Polyphen		128	154.44	0.82882		1943
Synonymous	0.00354	253	253	1.00	0.0000147	2182
Loss of Function	2.99	33	57.5	0.574	0.00000314	645

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00101	0.00101
Ashkenazi Jewish	0.000399	0.000397
East Asian	0.000707	0.000707
Finnish	0.00661	0.00663
European (Non-Finnish)	0.000609	0.000607
Middle Eastern	0.000707	0.000707
South Asian	0.000888	0.000882
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0983

Intolerance Scores

• rvis_EVS: 0.28
• rvis_percentile_EVS: 70.88

Haploinsufficiency Scores

• pHI: 0.0678
• hipred: N
• hipred_score: 0.414
• ghis: 0.602

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nrde2
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); skeleton phenotype

Gene ontology

• Biological process: biological_process;RNA interference;chromatin silencing by small RNA
• Cellular component: cellular_component
• Molecular function: molecular_function