NWD2

NACHT and WD repeat domain containing 2, the group of WD repeat domain containing

Basic information

Region (hg38): 4:37244742-37449463

Previous symbols: [ "KIAA1239" ]

Links

ENSG00000174145 ∙ NCBI:57495 ∙ OMIM:620172 ∙ HGNC:29229 ∙ Uniprot:Q9ULI1 ∙ 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 NWD2 gene.

• Inborn genetic diseases (52 variants)
• not provided (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NWD2 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				9	1	10
missense			52		1	53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	9	2

Variants in NWD2

This is a list of pathogenic ClinVar variants found in the NWD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-37245084-C-T		not specified	Uncertain significance (Oct 07, 2022)
4-37245162-C-T		not specified	Uncertain significance (Nov 27, 2023)
4-37245194-G-A		not specified	Uncertain significance (Jul 26, 2022)
4-37356430-G-A		not specified	Uncertain significance (Dec 07, 2021)
4-37356447-A-C		not specified	Uncertain significance (Sep 01, 2021)
4-37356465-G-T		not specified	Uncertain significance (Mar 14, 2023)
4-37356475-G-C		not specified	Uncertain significance (Feb 28, 2024)
4-37430605-A-G		not specified	Uncertain significance (Nov 30, 2022)
4-37430647-G-A		not specified	Uncertain significance (May 24, 2023)
4-37430653-G-A		not specified	Uncertain significance (Dec 06, 2022)
4-37430654-C-T		not specified	Uncertain significance (Nov 08, 2022)
4-37430670-G-A			Likely benign (Dec 01, 2022)
4-37430678-A-C		not specified	Uncertain significance (Jan 03, 2022)
4-37430738-G-C		not specified	Uncertain significance (Apr 13, 2022)
4-37430754-G-A		not specified	Uncertain significance (Feb 14, 2023)
4-37430769-A-C		not specified	Uncertain significance (Nov 02, 2021)
4-37433889-C-T		not specified	Uncertain significance (Apr 18, 2023)
4-37433971-C-T			Likely benign (Mar 01, 2022)
4-37434009-A-T		not specified	Uncertain significance (Aug 14, 2023)
4-37438894-A-G		not specified	Uncertain significance (Aug 30, 2021)
4-37438963-G-A		not specified	Uncertain significance (Sep 25, 2023)
4-37438974-G-A		not specified	Uncertain significance (Nov 18, 2022)
4-37438978-A-T		not specified	Uncertain significance (Mar 13, 2023)
4-37439185-C-G		not specified	Uncertain significance (Dec 21, 2022)
4-37439221-A-G		not specified	Uncertain significance (Mar 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NWD2	protein_coding	protein_coding	ENST00000309447	7	205246

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.984	0.0161	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.77	509	915	0.556	0.0000480	11465
Missense in Polyphen		57	179.27	0.31795		2273
Synonymous	3.05	288	362	0.796	0.0000198	3392
Loss of Function	5.74	10	56.6	0.177	0.00000296	744

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.66

Haploinsufficiency Scores

• pHI: 0.874
• ghis: 0.419

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Nwd2

Gene ontology

• Biological process: ribosomal large subunit biogenesis
• Molecular function: unfolded protein binding