WDR90

WD repeat domain 90, the group of WD repeat domain containing

Basic information

Region (hg38): 16:649311-667833

Previous symbols: [ "C16orf17", "C16orf15", "C16orf16", "C16orf19", "C16orf18" ]

Links

ENSG00000161996 ∙ NCBI:197335 ∙ OMIM:618290 ∙ HGNC:26960 ∙ Uniprot:Q96KV7 ∙ 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 WDR90 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR90 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				6	1	7
missense			136	23	1	160
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	136	29	2

Variants in WDR90

This is a list of pathogenic ClinVar variants found in the WDR90 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-649420-G-C		not specified	Uncertain significance (Dec 21, 2022)
16-649774-C-T		not specified	Uncertain significance (Jul 12, 2023)
16-650046-A-G		not specified	Uncertain significance (Jun 30, 2022)
16-650060-C-T		not specified	Uncertain significance (Jan 23, 2024)
16-650073-C-T		not specified	Uncertain significance (Aug 02, 2023)
16-650079-C-T		not specified	Uncertain significance (Oct 03, 2024)
16-650090-A-G		not specified	Uncertain significance (Dec 28, 2023)
16-650094-G-A		not specified	Uncertain significance (Jun 22, 2021)
16-650121-C-T		not specified	Uncertain significance (Apr 26, 2023)
16-650160-C-T		not specified	Uncertain significance (Mar 24, 2023)
16-650166-A-G		not specified	Uncertain significance (Jan 23, 2024)
16-650287-C-G		not specified	Uncertain significance (Aug 09, 2021)
16-650287-C-T		not specified	Uncertain significance (Jan 10, 2022)
16-650344-G-A		not specified	Uncertain significance (Dec 13, 2021)
16-650565-G-T		not specified	Uncertain significance (May 03, 2023)
16-650631-G-A		not specified	Likely benign (Oct 03, 2022)
16-650662-G-C		not specified	Uncertain significance (Jun 25, 2024)
16-650988-C-T			Likely benign (Mar 01, 2023)
16-651088-G-A		not specified	Likely benign (Apr 25, 2022)
16-651102-C-T		not specified	Uncertain significance (Dec 07, 2021)
16-651217-G-T			Likely benign (Mar 01, 2023)
16-651237-T-C		not specified	Uncertain significance (Dec 27, 2022)
16-651680-C-T		not specified	Uncertain significance (May 01, 2024)
16-651698-C-G		not specified	Uncertain significance (Aug 12, 2024)
16-651725-T-C		not specified	Uncertain significance (Dec 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR90	protein_coding	protein_coding	ENST00000293879	41	18523

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.26e-64	1.33e-11	124268	4	658	124930	0.00265

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.926	1208	1.12e+3	1.08	0.0000755	11093
Missense in Polyphen		415	379.27	1.0942		4130
Synonymous	-4.84	649	510	1.27	0.0000389	3703
Loss of Function	-0.785	93	85.2	1.09	0.00000435	874

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0101	0.00985
Ashkenazi Jewish	0.0000997	0.0000993
East Asian	0.00209	0.00200
Finnish	0.000547	0.000510
European (Non-Finnish)	0.00251	0.00231
Middle Eastern	0.00209	0.00200
South Asian	0.00186	0.00180
Other	0.00173	0.00165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for efficient primary cilium formation. {ECO:0000269|PubMed:28781053}.

Intolerance Scores

• loftool: 0.934
• rvis_EVS: 0.97
• rvis_percentile_EVS: 90.28

Haploinsufficiency Scores

• pHI: 0.125
• hipred: N
• hipred_score: 0.146
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.476

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr90

Gene ontology

• Biological process: cilium assembly
• Cellular component: centriole
• Molecular function: protein binding