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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 19.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_001007525.5	NP_001007526.3	17	yes	-
ENST00000524140.7	ENSP00000428579.2	17	yes	-
NM_001290355.3	NP_001277284.1	16	-	-
NM_001347994.1	NP_001334923.1	15	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NWD1 gene.

• not_specified (255 variants)
• not_provided (13 variants)
• Prostate_cancer (1 variants)

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. These statistics are base on transcript: NM_001007525.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	4	1	7
missense			242	20	5	267
nonsense			2			2
start loss						0
frameshift				1		1
splice donor/acceptor (+/-2bp)			3			3
Total	0	0	249	25	6

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
		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

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

Gene ontology

• Cellular component: cytosol
• Molecular function: ATP binding