WDSUB1

WD repeat, sterile alpha motif and U-box domain containing 1, the group of WD repeat domain containing|Sterile alpha motif domain containing|U-box domain containing

Basic information

Region (hg38): 2:159235798-159286703

Previous symbols: [ "WDSAM1" ]

Links

ENSG00000196151 ∙ NCBI:151525 ∙ ∙ HGNC:26697 ∙ Uniprot:Q8N9V3 ∙ 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 WDSUB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDSUB1 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						0
missense			22	3		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	3	0

Variants in WDSUB1

This is a list of pathogenic ClinVar variants found in the WDSUB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-159236044-G-A		not specified	Uncertain significance (Jan 23, 2023)
2-159236061-T-C		not specified	Uncertain significance (Aug 28, 2023)
2-159236082-C-G		not specified	Uncertain significance (Jul 12, 2022)
2-159236100-G-A		not specified	Likely benign (Aug 04, 2021)
2-159248386-G-A		not specified	Uncertain significance (Mar 23, 2023)
2-159248405-T-C		not specified	Uncertain significance (Mar 18, 2024)
2-159248426-C-T		not specified	Uncertain significance (Nov 21, 2022)
2-159256220-T-G		not specified	Uncertain significance (Jan 03, 2024)
2-159256246-T-C		not specified	Likely benign (Jan 18, 2023)
2-159256261-T-C		not specified	Uncertain significance (Dec 22, 2023)
2-159256372-C-G		not specified	Uncertain significance (Sep 16, 2021)
2-159257797-C-T		not specified	Uncertain significance (Sep 01, 2021)
2-159259824-T-C		not specified	Uncertain significance (Oct 16, 2023)
2-159271712-G-C		not specified	Uncertain significance (Dec 15, 2022)
2-159271780-T-C		not specified	Uncertain significance (Jul 09, 2021)
2-159279893-C-T		not specified	Uncertain significance (Jun 06, 2023)
2-159282733-C-T		not specified	Likely benign (Mar 20, 2024)
2-159282741-G-A		not specified	Uncertain significance (Feb 16, 2023)
2-159282766-C-T		not specified	Uncertain significance (Jul 12, 2023)
2-159282783-C-G		not specified	Uncertain significance (Mar 07, 2024)
2-159282795-A-C		not specified	Uncertain significance (Aug 15, 2023)
2-159282870-T-A		not specified	Uncertain significance (Aug 02, 2022)
2-159282929-A-T		not specified	Uncertain significance (Jun 11, 2024)
2-159282933-G-A		not specified	Uncertain significance (Dec 27, 2023)
2-159282952-G-T		not specified	Likely benign (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDSUB1	protein_coding	protein_coding	ENST00000409990	10	51007

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.75e-14	0.0322	125616	0	132	125748	0.000525

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.343	232	247	0.939	0.0000122	3102
Missense in Polyphen		99	108.31	0.91401		1372
Synonymous	0.929	81	92.4	0.877	0.00000488	906
Loss of Function	0.244	21	22.2	0.944	0.00000100	292

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000975	0.000971
Ashkenazi Jewish	0.000220	0.000198
East Asian	0.000492	0.000489
Finnish	0.00	0.00
European (Non-Finnish)	0.000786	0.000765
Middle Eastern	0.000492	0.000489
South Asian	0.000349	0.000327
Other	0.000694	0.000652

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.210

Intolerance Scores

• loftool: 0.767
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.49

Haploinsufficiency Scores

• pHI: 0.348
• hipred: N
• hipred_score: 0.350
• ghis: 0.520

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0168

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdsub1

Gene ontology

• Biological process: protein ubiquitination
• Molecular function: ubiquitin-protein transferase activity