WDR13

WD repeat domain 13, the group of WD repeat domain containing

Basic information

Region (hg38): X:48590042-48608869

Links

ENSG00000101940 ∙ NCBI:64743 ∙ OMIM:300512 ∙ HGNC:14352 ∙ Uniprot:Q9H1Z4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability (Limited), mode of inheritance: XL

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the WDR13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR13 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	2	5
missense			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	13	4	2

Variants in WDR13

This is a list of pathogenic ClinVar variants found in the WDR13 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-48598770-G-T		not specified	Uncertain significance (Jan 18, 2023)
X-48598791-G-A		not specified	Uncertain significance (Jun 17, 2024)
X-48599393-A-G		not specified	Conflicting classifications of pathogenicity (Mar 01, 2023)
X-48599455-G-A		not specified	Uncertain significance (Dec 28, 2023)
X-48599646-A-G		not specified	Uncertain significance (Dec 31, 2023)
X-48599665-C-T			Likely benign (Jan 08, 2018)
X-48599705-G-A		not specified	Uncertain significance (Jan 05, 2022)
X-48600374-C-T			Likely benign (Dec 01, 2022)
X-48600377-C-T			Likely benign (May 14, 2018)
X-48600491-C-T			Benign (Apr 05, 2018)
X-48600516-A-G		not specified	Uncertain significance (Dec 11, 2023)
X-48600589-G-C		not specified	Uncertain significance (Apr 22, 2022)
X-48601793-G-A		not specified	Uncertain significance (Jan 17, 2023)
X-48601844-G-T		not specified	Conflicting classifications of pathogenicity (Apr 20, 2023)
X-48601863-C-T		Esophageal atresia;Pyloric stenosis	Uncertain significance (May 22, 2019)
X-48601902-G-A		not specified	Uncertain significance (May 30, 2023)
X-48601914-C-T		not specified	Uncertain significance (May 17, 2023)
X-48601934-G-A			Likely benign (Aug 16, 2017)
X-48601956-T-G		not specified	Uncertain significance (Jan 23, 2024)
X-48604266-T-C			Likely benign (Sep 01, 2023)
X-48604315-C-T		not specified	Uncertain significance (Jun 16, 2024)
X-48604318-A-G		not specified	Uncertain significance (Jan 25, 2023)
X-48604320-C-T			Benign (Jul 07, 2018)
X-48604331-C-T		not specified	Uncertain significance (Oct 05, 2023)
X-48604343-G-A		not specified	Uncertain significance (Mar 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR13	protein_coding	protein_coding	ENST00000218056	9	15152

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.935	0.0648	125201	0	1	125202	0.00000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.29	95	238	0.399	0.0000229	3151
Missense in Polyphen		10	67.672	0.14777		906
Synonymous	0.153	95	96.9	0.980	0.00000905	1021
Loss of Function	3.10	1	13.1	0.0764	9.88e-7	210

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)	0.0000123	0.00000884
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0967

Intolerance Scores

• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.09

Haploinsufficiency Scores

• pHI: 0.141
• hipred: Y
• hipred_score: 0.662
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.180

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr13
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: negative regulation of type B pancreatic cell proliferation
• Cellular component: nucleoplasm;microtubule organizing center;plasma membrane
• Molecular function: promoter-specific chromatin binding