WDR38

WD repeat domain 38, the group of WD repeat domain containing

Basic information

Region (hg38): 9:124853417-124857890

Links

ENSG00000136918 ∙ NCBI:401551 ∙ ∙ HGNC:23745 ∙ Uniprot:Q5JTN6 ∙ 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 WDR38 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR38 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			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	21	1	1

Variants in WDR38

This is a list of pathogenic ClinVar variants found in the WDR38 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-124853557-T-C		not specified	Uncertain significance (Feb 05, 2024)
9-124854209-A-G		not specified	Uncertain significance (Aug 30, 2022)
9-124854256-G-C		not specified	Uncertain significance (Sep 27, 2024)
9-124855647-C-A		not specified	Uncertain significance (Mar 06, 2023)
9-124855681-A-G		not specified	Uncertain significance (Jun 18, 2024)
9-124855705-C-T		not specified	Uncertain significance (Aug 28, 2024)
9-124855716-T-G		not specified	Uncertain significance (Oct 04, 2024)
9-124855727-C-T		not specified	Uncertain significance (Nov 10, 2022)
9-124855868-A-T		not specified	Uncertain significance (Jun 29, 2022)
9-124855888-G-C		not specified	Uncertain significance (Aug 20, 2024)
9-124855914-G-A		not specified	Uncertain significance (Dec 20, 2023)
9-124855935-C-T		not specified	Uncertain significance (Apr 05, 2023)
9-124856244-G-A		not specified	Uncertain significance (Jan 18, 2023)
9-124856256-G-A		not specified	Uncertain significance (May 03, 2023)
9-124856270-C-T		not specified	Uncertain significance (Oct 20, 2021)
9-124856273-C-T		not specified	Uncertain significance (Sep 17, 2021)
9-124856274-G-A		not specified	Uncertain significance (Mar 21, 2024)
9-124856278-C-G		not specified	Uncertain significance (Jul 16, 2024)
9-124856289-G-A		not specified	Uncertain significance (Apr 12, 2024)
9-124856294-G-A		not specified	Uncertain significance (Apr 12, 2024)
9-124856542-C-T		not specified	Uncertain significance (Feb 27, 2023)
9-124856570-C-G		not specified	Uncertain significance (Mar 15, 2024)
9-124856738-G-A		not specified	Uncertain significance (Oct 20, 2024)
9-124856829-T-C		not specified	Uncertain significance (Dec 21, 2023)
9-124856847-A-G		not specified	Likely benign (May 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR38	protein_coding	protein_coding	ENST00000373574	9	4406

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.97e-11	0.0345	124665	0	150	124815	0.000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.347	172	185	0.928	0.0000115	2013
Missense in Polyphen		58	59.88	0.96861		715
Synonymous	-0.201	79	76.8	1.03	0.00000498	632
Loss of Function	-0.189	16	15.2	1.05	6.54e-7	165

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00354	0.00353
Ashkenazi Jewish	0.00	0.00
East Asian	0.000335	0.000334
Finnish	0.00121	0.00121
European (Non-Finnish)	0.000415	0.000397
Middle Eastern	0.000335	0.000334
South Asian	0.000164	0.000163
Other	0.000827	0.000824

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.569
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.21

Haploinsufficiency Scores

• pHI: 0.127
• hipred: N
• hipred_score: 0.131
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.280

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr38