NWD1

NACHT and WD repeat domain containing 1, the group of WD repeat domain containing

Basic information

Region (hg38): 19:16719847-16817963

Links

ENSG00000188039 ∙ NCBI:284434 ∙ OMIM:616250 ∙ HGNC:27619 ∙ Uniprot:Q149M9 ∙ 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 NWD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NWD1 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				3	1	4
missense			106	6	5	117
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	106	10	6

Variants in NWD1

This is a list of pathogenic ClinVar variants found in the NWD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-16731213-C-A		not specified	Uncertain significance (Jul 08, 2022)
19-16731220-G-A		not specified	Uncertain significance (May 31, 2022)
19-16731256-A-G		not specified	Uncertain significance (Oct 27, 2023)
19-16736658-C-T		not specified	Uncertain significance (Apr 04, 2023)
19-16736680-A-G		not specified	Uncertain significance (Jan 26, 2023)
19-16744452-T-A		not specified	Uncertain significance (Dec 06, 2023)
19-16744463-C-T		not specified	Uncertain significance (Feb 16, 2023)
19-16744479-A-C		not specified	Uncertain significance (Nov 10, 2022)
19-16744508-G-T		not specified	Uncertain significance (Dec 15, 2023)
19-16744548-A-T		not specified	Uncertain significance (Dec 19, 2023)
19-16744556-G-A		not specified	Uncertain significance (Oct 02, 2023)
19-16744571-C-T		not specified	Uncertain significance (Jul 05, 2023)
19-16744580-G-A		not specified	Likely benign (Nov 09, 2021)
19-16744600-T-TG			Likely benign (Apr 01, 2023)
19-16744644-T-C		not specified	Uncertain significance (Dec 19, 2022)
19-16744667-C-T		not specified	Likely benign (Dec 16, 2023)
19-16744668-G-A		not specified	Uncertain significance (Dec 12, 2023)
19-16744671-G-T		not specified	Uncertain significance (Jul 12, 2022)
19-16749163-G-A		not specified	Uncertain significance (Nov 30, 2022)
19-16749171-A-T		not specified	Uncertain significance (May 26, 2024)
19-16749172-G-A		not specified	Uncertain significance (Dec 01, 2022)
19-16749183-C-T			Likely benign (Oct 01, 2022)
19-16749190-A-T			Benign (Oct 10, 2018)
19-16749201-G-A		not specified	Uncertain significance (Oct 03, 2024)
19-16749211-G-A		not specified	Uncertain significance (Jun 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NWD1	protein_coding	protein_coding	ENST00000524140	17	97988

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.49e-26	0.0544	125338	3	406	125747	0.00163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.162	844	857	0.984	0.0000535	9187
Missense in Polyphen		183	193.8	0.94429		2255
Synonymous	0.383	372	382	0.975	0.0000250	3034
Loss of Function	1.65	48	62.0	0.774	0.00000322	647

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0131	0.0129
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.00163	0.00163
Finnish	0.0000930	0.0000924
European (Non-Finnish)	0.000767	0.000739
Middle Eastern	0.00163	0.00163
South Asian	0.00178	0.00177
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the control of androgen receptor (AR) protein steady-state levels. {ECO:0000269|PubMed:24681825}.

Intolerance Scores

• loftool: 0.937
• rvis_EVS: 1.76
• rvis_percentile_EVS: 96.74

Haploinsufficiency Scores

• pHI: 0.127
• hipred: N
• hipred_score: 0.123
• ghis: 0.436

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0950

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nwd1

Gene ontology

• Cellular component: cytosol
• Molecular function: ATP binding