WDR7

WD repeat domain 7, the group of Armadillo like helical domain containing|WD repeat domain containing

Basic information

Region (hg38): 18:56651343-57029811

Links

ENSG00000091157 ∙ NCBI:23335 ∙ OMIM:613473 ∙ HGNC:13490 ∙ Uniprot:Q9Y4E6 ∙ 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 WDR7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR7 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				4	4	8
missense			63	2		65
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region					1	1
non coding						0
Total	0	0	64	6	4

Variants in WDR7

This is a list of pathogenic ClinVar variants found in the WDR7 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-56672618-G-A		not specified	Uncertain significance (Nov 03, 2022)
18-56682707-G-A		not specified	Uncertain significance (Jul 31, 2023)
18-56682729-C-T			Likely benign (Feb 01, 2023)
18-56682774-A-C		not specified	Uncertain significance (May 13, 2024)
18-56685981-G-A			Benign (Apr 24, 2018)
18-56686894-T-A		not specified	Uncertain significance (Feb 22, 2023)
18-56686961-C-G		not specified	Uncertain significance (Oct 12, 2022)
18-56691237-T-A		not specified	Uncertain significance (Nov 15, 2021)
18-56694662-G-T		not specified	Uncertain significance (Feb 28, 2023)
18-56694727-T-A		not specified	Uncertain significance (May 28, 2024)
18-56694739-G-A		not specified	Uncertain significance (Dec 27, 2022)
18-56694748-G-A		not specified	Uncertain significance (Jun 28, 2022)
18-56694985-G-A		not specified	Uncertain significance (May 05, 2023)
18-56695002-T-C			Likely benign (Jun 27, 2018)
18-56695046-A-G		not specified	Uncertain significance (Jun 14, 2023)
18-56695115-G-A		not specified	Uncertain significance (Jun 21, 2022)
18-56696286-A-G		not specified	Uncertain significance (Jun 07, 2023)
18-56718003-C-T		not specified	Uncertain significance (Oct 14, 2023)
18-56718114-G-A		not specified	Uncertain significance (Mar 24, 2023)
18-56718136-T-C		not specified	Uncertain significance (Dec 09, 2023)
18-56731419-T-C		not specified	Uncertain significance (Mar 07, 2023)
18-56731505-A-T		not specified	Uncertain significance (May 20, 2024)
18-56756579-A-G			Benign (Dec 31, 2019)
18-56756625-G-T		WDR7-related disorder	Likely benign (Apr 28, 2022)
18-56756649-C-G		not specified	Uncertain significance (Jun 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR7	protein_coding	protein_coding	ENST00000254442	27	380255

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	1.13e-7	125728	0	20	125748	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.48	639	842	0.759	0.0000462	9682
Missense in Polyphen		245	376.06	0.6515		4181
Synonymous	0.496	300	311	0.964	0.0000186	3005
Loss of Function	7.44	8	79.6	0.101	0.00000460	881

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000374	0.000364
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000618	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.258
• rvis_EVS: -2.3
• rvis_percentile_EVS: 1.22

Haploinsufficiency Scores

• pHI: 0.291
• hipred: Y
• hipred_score: 0.749
• ghis: 0.631

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.820

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr7

Gene ontology

• Biological process: hematopoietic progenitor cell differentiation
• Cellular component: synaptic vesicle