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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 6.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_001291088.2	NP_001278017.1	5	yes	-
ENST00000447313.7	ENSP00000405012.2	5	yes	-
NM_031951.5	NP_114157.4	5	-	-
ENST00000303868.5	ENSP00000368025.3	5	-	-

Phenotypes

GenCC

Source: genCC

• cataract (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the WDR87 gene.

• not_specified (404 variants)
• not_provided (226 variants)
• EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

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. These statistics are base on transcript: NM_001291088.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	44	11	56
missense			405	69	16	490
nonsense			6	2	1	9
start loss						0
frameshift			4		1	5
splice donor/acceptor (+/-2bp)						0
Total	0	0	416	115	29

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
		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

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