WDR18

WD repeat domain 18, the group of WD repeat domain containing|Large ribosomal subunit biogenesis complex

Basic information

Region (hg38): 19:984332-998438

Links

ENSG00000065268 ∙ NCBI:57418 ∙ OMIM:620291 ∙ HGNC:17956 ∙ Uniprot:Q9BV38 ∙ 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 WDR18 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR18 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			52			52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	0	1

Variants in WDR18

This is a list of pathogenic ClinVar variants found in the WDR18 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-984367-T-C		not specified	Uncertain significance (May 30, 2024)
19-984368-G-C		not specified	Uncertain significance (Sep 01, 2021)
19-984382-G-T		not specified	Uncertain significance (Nov 27, 2024)
19-984416-C-G		not specified	Uncertain significance (May 17, 2023)
19-984467-G-C		not specified	Uncertain significance (Dec 27, 2023)
19-984487-C-G		not specified	Uncertain significance (May 29, 2024)
19-984552-C-T		not specified	Uncertain significance (Nov 26, 2024)
19-984557-G-C		not specified	Uncertain significance (Feb 15, 2023)
19-985887-T-C		not specified	Uncertain significance (Oct 04, 2022)
19-985895-G-C		not specified	Uncertain significance (Mar 29, 2024)
19-985914-C-T		not specified	Uncertain significance (May 29, 2024)
19-985958-A-G		not specified	Uncertain significance (Mar 29, 2022)
19-985970-T-C		not specified	Uncertain significance (Mar 06, 2023)
19-989777-C-T		not specified	Uncertain significance (Oct 12, 2022)
19-989796-G-A		not specified	Uncertain significance (Dec 20, 2023)
19-989809-C-G		not specified	Uncertain significance (Dec 07, 2023)
19-989831-G-A		not specified	Uncertain significance (Nov 02, 2023)
19-989888-C-T		not specified	Uncertain significance (Jul 06, 2021)
19-990224-G-A		not specified	Uncertain significance (Aug 04, 2024)
19-990233-G-T		not specified	Uncertain significance (Jun 06, 2023)
19-990265-C-G		not specified	Uncertain significance (Dec 05, 2024)
19-990266-G-T		not specified	Uncertain significance (Aug 16, 2022)
19-990308-G-A		not specified	Uncertain significance (Oct 26, 2022)
19-990326-G-A		not specified	Uncertain significance (May 10, 2024)
19-990860-G-C		not specified	Uncertain significance (Apr 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR18	protein_coding	protein_coding	ENST00000251289	10	11396

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00729	125511	0	21	125532	0.0000836

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.479	232	253	0.915	0.0000161	2734
Missense in Polyphen		66	71.135	0.92781		749
Synonymous	-1.52	138	117	1.18	0.00000846	879
Loss of Function	3.84	1	19.1	0.0524	8.88e-7	214

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000265	0.000265
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000384	0.000231
European (Non-Finnish)	0.0000550	0.0000529
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a component of the Five Friends of Methylated CHTOP (5FMC) complex; the 5FMC complex is recruited to ZNF148 by methylated CHTOP, leading to desumoylation of ZNF148 and subsequent transactivation of ZNF148 target genes (PubMed:22872859). Component of the PELP1 complex involved in the nucleolar steps of 28S rRNA maturation and the subsequent nucleoplasmic transit of the pre-60S ribosomal subunit (PubMed:21326211). {ECO:0000269|PubMed:21326211, ECO:0000269|PubMed:22872859}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.298
• rvis_EVS: 0
• rvis_percentile_EVS: 53.85

Haploinsufficiency Scores

• pHI: 0.109
• hipred: Y
• hipred_score: 0.783
• ghis: 0.540

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.906

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr18

Zebrafish Information Network

• Gene name: wdr18
• Affected structure: pancreas
• Phenotype tag: abnormal
• Phenotype quality: mislocalised

Gene ontology

• Biological process: ribosomal large subunit assembly;pre-replicative complex assembly involved in nuclear cell cycle DNA replication;rRNA processing;multicellular organism development;regulation of DNA-dependent DNA replication initiation
• Cellular component: nucleoplasm;nuclear pre-replicative complex;nucleolus;cytoplasm;Rix1 complex
• Molecular function: protein binding