WDR73

WD repeat domain 73, the group of WD repeat domain containing

Basic information

Region (hg38): 15:84639284-84654343

Links

ENSG00000177082 ∙ NCBI:84942 ∙ OMIM:616144 ∙ HGNC:25928 ∙ Uniprot:Q6P4I2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Galloway-Mowat syndrome 1 (Strong), mode of inheritance: AR
• Galloway-Mowat syndrome (Supportive), mode of inheritance: AR
• CAMOS syndrome (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Galloway-Mowat syndrome 1	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic; Renal	25466283; 25873735; 26123727

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the WDR73 gene.

• not provided (131 variants)
• Galloway-Mowat syndrome 1 (42 variants)
• Inborn genetic diseases (25 variants)
• not specified (2 variants)
• Nephrotic syndrome (2 variants)
• Abnormality of the nervous system (1 variants)
• WDR73-related condition (1 variants)
• - (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR73 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				22	4	26
missense		4	56	2	4	66
nonsense	1	5	3			9
start loss			1			1
frameshift	5	5				10
inframe indel			2		1	3
splice donor/acceptor (+/-2bp)		1				1
splice region			4	4	1	9
non coding			1	17	12	30
Total	6	15	63	41	21

Highest pathogenic variant AF is 0.0000525

Variants in WDR73

This is a list of pathogenic ClinVar variants found in the WDR73 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-84643298-T-A			Benign (Mar 02, 2020)
15-84643346-C-T			Benign (Aug 20, 2019)
15-84643406-G-C			Benign (Nov 12, 2018)
15-84643474-C-T			Uncertain significance (Dec 18, 2023)
15-84643474-CG-C		not specified	Conflicting classifications of pathogenicity (Oct 25, 2022)
15-84643474-C-CG		Galloway-Mowat syndrome 1 • WDR73-related disorder	Conflicting classifications of pathogenicity (Oct 13, 2023)
15-84643475-G-A		Galloway-Mowat syndrome 1	Uncertain significance (Jul 25, 2022)
15-84643475-G-T			Uncertain significance (Jan 02, 2024)
15-84643477-G-A		Galloway-Mowat syndrome 1	Uncertain significance (Apr 19, 2022)
15-84643479-G-A			Likely benign (Aug 17, 2022)
15-84643480-G-C		Inborn genetic diseases	Uncertain significance (Feb 17, 2022)
15-84643481-C-A		Inborn genetic diseases • WDR73-related disorder	Conflicting classifications of pathogenicity (Nov 27, 2023)
15-84643481-C-T			Uncertain significance (Apr 18, 2022)
15-84643491-C-T			Likely benign (Jul 17, 2023)
15-84643501-C-T		Galloway-Mowat syndrome 1	Uncertain significance (Jun 29, 2022)
15-84643509-CAG-C		Galloway-Mowat syndrome 1	Likely pathogenic (Mar 05, 2022)
15-84643510-A-G			Uncertain significance (Jan 11, 2021)
15-84643517-C-T			Uncertain significance (Jun 07, 2022)
15-84643534-A-G		Inborn genetic diseases	Uncertain significance (Aug 11, 2022)
15-84643545-T-C			Likely benign (Nov 01, 2022)
15-84643554-G-C			Likely benign (Nov 16, 2023)
15-84643561-C-T			Likely pathogenic (Jan 31, 2019)
15-84643568-G-A		Galloway-Mowat syndrome 1	Pathogenic (Jun 29, 2015)
15-84643569-G-A		WDR73-related disorder	Likely benign (Jun 13, 2019)
15-84643589-G-T			Uncertain significance (Aug 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR73	protein_coding	protein_coding	ENST00000434634	8	11576

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.82e-9	0.293	124577	0	69	124646	0.000277

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.461	225	206	1.09	0.0000110	2388
Missense in Polyphen		62	68.123	0.91011		844
Synonymous	0.128	76	77.4	0.981	0.00000391	758
Loss of Function	0.722	15	18.3	0.818	9.94e-7	204

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000252	0.000250
Ashkenazi Jewish	0.00	0.00
East Asian	0.000612	0.000612
Finnish	0.00	0.00
European (Non-Finnish)	0.000272	0.000265
Middle Eastern	0.000612	0.000612
South Asian	0.000697	0.000686
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the regulation of microtubule organization and dynamics (PubMed:25466283). {ECO:0000269|PubMed:25466283}.
• Disease: DISEASE: Galloway-Mowat syndrome 1 (GAMOS1) [MIM:251300]: A form of Galloway-Mowat syndrome, a severe renal-neurological disease characterized by early-onset nephrotic syndrome associated with microcephaly, central nervous system abnormalities, developmental delays, and a propensity for seizures. Brain anomalies include gyration defects ranging from lissencephaly to pachygyria and polymicrogyria, and cerebellar hypoplasia. Most patients show facial dysmorphism characterized by a small, narrow forehead, large/floppy ears, deep-set eyes, hypertelorism and micrognathia. Additional variable features are visual impairment and arachnodactyly. Patients may die in early childhood. GAMOS1 inheritance is autosomal recessive. {ECO:0000269|PubMed:25466283}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Intolerance Scores

• loftool: 0.828
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.59

Haploinsufficiency Scores

• pHI: 0.104
• hipred: N
• hipred_score: 0.144
• ghis: 0.453

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.596

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr73

Zebrafish Information Network

• Gene name: wdr73
• Affected structure: ventricular system
• Phenotype tag: abnormal
• Phenotype quality: dilated

Gene ontology

• Biological process: nucleus organization;cytoplasmic microtubule organization;negative regulation of apoptotic process
• Cellular component: spindle pole;cytosol;cleavage furrow
• Molecular function: molecular_function