WDR20

WD repeat domain 20, the group of WD repeat domain containing

Basic information

Region (hg38): 14:102139503-102224847

Links

ENSG00000140153 ∙ NCBI:91833 ∙ OMIM:617741 ∙ HGNC:19667 ∙ Uniprot:Q8TBZ3 ∙ 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 WDR20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR20 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			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	0

Variants in WDR20

This is a list of pathogenic ClinVar variants found in the WDR20 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-102139930-A-G		not specified	Uncertain significance (Jun 04, 2024)
14-102140045-A-G		not specified	Uncertain significance (Apr 07, 2023)
14-102140128-G-A		not specified	Uncertain significance (Nov 30, 2022)
14-102140161-G-A		not specified	Uncertain significance (Dec 02, 2022)
14-102195008-A-G		not specified	Uncertain significance (Jun 27, 2022)
14-102195040-C-T		not specified	Uncertain significance (Mar 28, 2023)
14-102197836-G-GTAAC		Global developmental delay;Delayed speech and language development;Dolichocephaly	Uncertain significance (Jul 11, 2024)
14-102208648-G-A		not specified	Uncertain significance (Dec 28, 2022)
14-102208714-A-G		not specified	Uncertain significance (Apr 07, 2023)
14-102208771-G-A		not specified	Uncertain significance (Jun 22, 2023)
14-102208807-C-T		not specified	Uncertain significance (Jul 19, 2022)
14-102208810-C-T		not specified	Uncertain significance (Dec 12, 2023)
14-102208828-G-A		not specified	Uncertain significance (Aug 10, 2023)
14-102208864-G-T		not specified	Uncertain significance (Apr 12, 2022)
14-102208872-C-A		not specified	Uncertain significance (May 08, 2024)
14-102208904-G-A		not specified	Uncertain significance (Jun 16, 2024)
14-102208994-A-G		not specified	Uncertain significance (Mar 06, 2023)
14-102208999-A-G		not specified	Uncertain significance (Nov 19, 2022)
14-102209153-G-T		not specified	Uncertain significance (Oct 04, 2022)
14-102209161-G-A		not specified	Uncertain significance (Sep 01, 2021)
14-102209365-A-G		not specified	Uncertain significance (Feb 28, 2024)
14-102209386-G-A		not specified	Uncertain significance (Nov 02, 2023)
14-102209401-G-C		not specified	Uncertain significance (Dec 18, 2023)
14-102209419-A-G		not specified	Uncertain significance (May 20, 2024)
14-102209485-G-T		not specified	Uncertain significance (Dec 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR20	protein_coding	protein_coding	ENST00000454394	4	85345

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.915	0.0847	125743	0	2	125745	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.85	243	339	0.718	0.0000191	3966
Missense in Polyphen		38	91.413	0.41569		1053
Synonymous	-0.219	143	140	1.02	0.00000901	1201
Loss of Function	3.66	3	21.1	0.142	0.00000131	233

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)	0.0000179	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator of deubiquitinating complexes. Activates deubiquitinating activity of complexes containing USP12 (PubMed:20147737, PubMed:27373336). Anchors at the base of the ubiquitin-contacting loop of USP12 and remotely modulates the catalytic center of the enzyme (PubMed:27373336). {ECO:0000269|PubMed:20147737, ECO:0000269|PubMed:27373336}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Ub-specific processing proteases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.293

Intolerance Scores

• loftool: 0.0269
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.56

Haploinsufficiency Scores

• pHI: 0.425
• hipred: Y
• hipred_score: 0.693
• ghis: 0.643

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.793

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr20

Gene ontology

• Biological process: protein deubiquitination
• Cellular component: nucleoplasm
• Molecular function: protein binding;thiol-dependent ubiquitinyl hydrolase activity