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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 32.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_001142551.2	NP_001136023.1	14	yes	-
ENST00000369962.8	ENSP00000358979.3	14	yes	-
NM_014969.6	NP_055784.3	14	-	-
NM_001142550.2	NP_001136022.1	14	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the WDR47 gene.

• not_specified (73 variants)
• not_provided (1 variants)
• Neurodevelopmental_disorder (1 variants)
• Complex_neurodevelopmental_disorder (1 variants)
• See_cases (1 variants)

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. These statistics are base on transcript: NM_001142551.2. 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	1		2
missense		2	77	1		80
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3			3
Total	0	2	81	2	0

Highest pathogenic variant AF is 0.000002478241

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
		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

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

Gene ontology

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