WDR89

WD repeat domain 89, the group of WD repeat domain containing

Basic information

Region (hg38): 14:63597039-63641871

Previous symbols: [ "C14orf150" ]

Links

ENSG00000140006 ∙ NCBI:112840 ∙ ∙ HGNC:20489 ∙ Uniprot:Q96FK6 ∙ 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 WDR89 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR89 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in WDR89

This is a list of pathogenic ClinVar variants found in the WDR89 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-63598822-C-T		not specified	Uncertain significance (Nov 22, 2022)
14-63598828-C-T		not specified	Uncertain significance (Aug 28, 2024)
14-63598838-C-T		not specified	Uncertain significance (Sep 16, 2021)
14-63598882-T-C		not specified	Uncertain significance (Mar 24, 2023)
14-63598917-A-T		not specified	Uncertain significance (Dec 22, 2023)
14-63598931-T-C		not specified	Uncertain significance (Sep 10, 2024)
14-63598969-C-T		not specified	Uncertain significance (Sep 20, 2023)
14-63598970-G-A		not specified	Uncertain significance (Nov 13, 2024)
14-63598976-T-C		not specified	Uncertain significance (May 18, 2023)
14-63599024-T-C		not specified	Uncertain significance (Sep 22, 2023)
14-63599080-G-A		not specified	Uncertain significance (Feb 06, 2024)
14-63599086-G-C		not specified	Uncertain significance (Apr 14, 2023)
14-63599119-T-C		not specified	Uncertain significance (Mar 17, 2023)
14-63599173-C-T		not specified	Uncertain significance (Jul 14, 2022)
14-63599236-G-A		not specified	Uncertain significance (Dec 19, 2022)
14-63599297-T-C		not specified	Likely benign (Aug 21, 2024)
14-63599348-C-T		not specified	Uncertain significance (Jun 11, 2021)
14-63599362-A-G		not specified	Uncertain significance (Jun 03, 2024)
14-63599455-C-A		not specified	Uncertain significance (May 31, 2023)
14-63599512-A-C		not specified	Uncertain significance (Oct 29, 2024)
14-63599535-T-A		not specified	Uncertain significance (Dec 14, 2022)
14-63599597-T-C		not specified	Uncertain significance (May 09, 2023)
14-63599636-T-C		not specified	Uncertain significance (Jul 14, 2023)
14-63599642-C-T		not specified	Uncertain significance (Jun 16, 2024)
14-63599644-C-T		not specified	Uncertain significance (Oct 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR89	protein_coding	protein_coding	ENST00000394942	1	44823

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000748	0.765	125645	0	101	125746	0.000402

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.884	167	202	0.825	0.00000949	2556
Missense in Polyphen		22	37.507	0.58656		468
Synonymous	0.141	69	70.5	0.979	0.00000303	742
Loss of Function	1.10	8	12.1	0.659	6.74e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000632	0.000631
Ashkenazi Jewish	0.00159	0.00159
East Asian	0.000109	0.000109
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000370	0.000352
Middle Eastern	0.000109	0.000109
South Asian	0.000653	0.000653
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0962

Intolerance Scores

• loftool: 0.871
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.26

Haploinsufficiency Scores

• pHI: 0.261
• hipred: N
• hipred_score: 0.251
• ghis: 0.654

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.859

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr89