WDR87

WD repeat domain 87, the group of WD repeat domain containing|Armadillo like helical domain containing

Basic information

Region (hg38): 19:37884823-37906677

Links

ENSG00000171804 ∙ NCBI:83889 ∙ OMIM:620274 ∙ HGNC:29934 ∙ Uniprot:Q6ZQQ6 ∙ 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 WDR87 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR87 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				30	17	47
missense			178	34	26	238
nonsense			3	2	1	6
start loss						0
frameshift			3		1	4
inframe indel			6	3	2	11
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding				5	7	12
Total	0	0	190	74	54

Variants in WDR87

This is a list of pathogenic ClinVar variants found in the WDR87 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-37884828-C-CA			Benign (Aug 16, 2019)
19-37884949-C-T		not specified	Likely benign (Apr 06, 2024)
19-37884953-G-A			Likely benign (Jul 18, 2023)
19-37884994-G-C		not specified	Uncertain significance (Feb 22, 2023)
19-37885005-G-A		not specified	Uncertain significance (Apr 17, 2024)
19-37885026-C-T			Benign (Jan 26, 2024)
19-37885027-G-A		not specified	Uncertain significance (Sep 30, 2021)
19-37885039-C-T		not specified	Likely benign (Aug 15, 2023)
19-37885054-G-A		not specified	Uncertain significance (Dec 06, 2021)
19-37885084-C-T			Uncertain significance (Sep 07, 2022)
19-37885098-T-C			Benign (Oct 13, 2023)
19-37885110-G-A		not specified	Uncertain significance (May 31, 2023)
19-37885111-G-A		not specified	Uncertain significance (Aug 15, 2023)
19-37885149-C-T		not specified	Uncertain significance (Aug 31, 2022)
19-37885150-G-A			Uncertain significance (Jun 09, 2023)
19-37885190-G-A			Benign (Jan 26, 2024)
19-37885194-A-G		not specified	Uncertain significance (May 30, 2023)
19-37885289-G-A			Likely benign (Aug 30, 2021)
19-37885299-T-A		not specified	Uncertain significance (Jan 26, 2022)
19-37885329-C-T		not specified	Uncertain significance (Aug 10, 2021)
19-37885330-G-A			Uncertain significance (Jul 13, 2023)
19-37885344-C-T			Benign (Jan 26, 2024)
19-37885345-G-A			Benign (Jan 26, 2024)
19-37885389-T-C		not specified	Uncertain significance (Feb 15, 2023)
19-37885392-T-C			Uncertain significance (Jul 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR87	protein_coding	protein_coding	ENST00000303868	5	21855

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.16e-20	0.479	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.22	966	1.41e+3	0.684	0.0000721	18886
Missense in Polyphen		264	378.64	0.69724		4880
Synonymous	4.19	402	524	0.767	0.0000254	5405
Loss of Function	1.89	38	52.8	0.720	0.00000303	575

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 4.14
• rvis_percentile_EVS: 99.69

Haploinsufficiency Scores

• pHI: 0.0622

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0354

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: 4932431P20Rik