WDR47

WD repeat domain 47, the group of WD repeat domain containing

Basic information

Region (hg38): 1:108970214-109042113

Links

ENSG00000085433 ∙ NCBI:22911 ∙ OMIM:615734 ∙ HGNC:29141 ∙ Uniprot:O94967 ∙ 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 WDR47 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR47 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				1		1
missense		1	21	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	21	2	0

Variants in WDR47

This is a list of pathogenic ClinVar variants found in the WDR47 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-108971494-T-A		not specified	Uncertain significance (Jun 17, 2024)
1-108971521-T-C		not specified	Uncertain significance (Aug 02, 2022)
1-108971528-T-G		not specified	Uncertain significance (Apr 26, 2024)
1-108974684-G-C		not specified	Uncertain significance (May 09, 2023)
1-108974747-T-C			Likely benign (Aug 01, 2022)
1-108981798-A-G		not specified	Uncertain significance (Oct 16, 2023)
1-108982671-C-G		not specified	Uncertain significance (Jan 27, 2022)
1-108983401-T-G		See cases	Likely pathogenic (Dec 18, 2023)
1-108986527-G-C		not specified	Uncertain significance (Mar 25, 2024)
1-108986668-T-C		not specified	Uncertain significance (May 01, 2024)
1-108991277-G-C		not specified	Uncertain significance (Dec 27, 2023)
1-108991315-G-A		not specified	Uncertain significance (Aug 19, 2023)
1-108995586-C-T		not specified	Likely benign (Oct 14, 2021)
1-108995658-A-G		not specified	Uncertain significance (Apr 15, 2024)
1-108995667-G-A		not specified	Uncertain significance (Jun 29, 2023)
1-109002273-C-G		not specified	Uncertain significance (Oct 05, 2021)
1-109002332-T-C		not specified	Uncertain significance (Jun 07, 2023)
1-109004623-T-C		not specified	Uncertain significance (Apr 22, 2024)
1-109004639-C-T		not specified	Uncertain significance (Feb 14, 2023)
1-109004710-G-A		not specified	Uncertain significance (May 25, 2022)
1-109010989-C-T		not specified	Uncertain significance (May 25, 2022)
1-109011366-A-G		not specified	Uncertain significance (Jan 26, 2022)
1-109011468-C-T		Neurodevelopmental disorder	Likely pathogenic (Apr 04, 2024)
1-109011477-C-T		not specified	Uncertain significance (Mar 01, 2024)
1-109011579-T-C		not specified	Uncertain significance (Feb 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR47	protein_coding	protein_coding	ENST00000400794	14	72015

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.292	0.708	125735	0	12	125747	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.75	317	488	0.649	0.0000246	6100
Missense in Polyphen		77	187.62	0.4104		2301
Synonymous	-0.125	173	171	1.01	0.00000893	1754
Loss of Function	4.69	10	43.3	0.231	0.00000215	546

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000164	0.000163
Ashkenazi Jewish	0.00	0.00
East Asian	0.000125	0.000109
Finnish	0.0000523	0.0000462
European (Non-Finnish)	0.0000442	0.0000439
Middle Eastern	0.000125	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.266
• rvis_EVS: -0.76
• rvis_percentile_EVS: 13.45

Haploinsufficiency Scores

• pHI: 0.625
• hipred: Y
• hipred_score: 0.563
• ghis: 0.616

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.862

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr47
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: multicellular organism development
• Cellular component: cytoplasm;microtubule
• Molecular function: protein binding