WDR43

WD repeat domain 43, the group of WD repeat domain containing|UTPa subcomplex|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 2:28894666-28948219

Links

ENSG00000163811 ∙ NCBI:23160 ∙ OMIM:616195 ∙ HGNC:28945 ∙ Uniprot:Q15061 ∙ 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 WDR43 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR43 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						0
missense			31			31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	31	0	1

Variants in WDR43

This is a list of pathogenic ClinVar variants found in the WDR43 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-28894744-G-A		not specified	Uncertain significance (May 10, 2024)
2-28894793-C-T		not specified	Uncertain significance (Mar 31, 2023)
2-28894805-G-A		not specified	Uncertain significance (Dec 19, 2023)
2-28894834-A-T		not specified	Uncertain significance (Jan 08, 2024)
2-28894843-C-T		not specified	Uncertain significance (Sep 17, 2021)
2-28902107-T-G		not specified	Uncertain significance (Jan 31, 2022)
2-28906450-T-A			Benign (Aug 24, 2017)
2-28906500-A-C		not specified	Uncertain significance (Oct 12, 2021)
2-28906559-G-A		not specified	Uncertain significance (Nov 07, 2022)
2-28906570-C-G		not specified	Uncertain significance (Aug 22, 2023)
2-28912609-A-G		not specified	Uncertain significance (May 14, 2024)
2-28912610-G-A		not specified	Uncertain significance (Jun 27, 2022)
2-28912647-G-T		not specified	Uncertain significance (Dec 09, 2023)
2-28914120-A-G		not specified	Uncertain significance (Aug 09, 2021)
2-28917896-G-C		not specified	Uncertain significance (Jan 09, 2024)
2-28925079-G-T		not specified	Uncertain significance (Sep 20, 2023)
2-28925143-T-C		not specified	Uncertain significance (Dec 19, 2022)
2-28925151-G-T		not specified	Uncertain significance (Dec 05, 2022)
2-28927626-C-T		not specified	Uncertain significance (Jan 10, 2023)
2-28927630-A-C		not specified	Uncertain significance (Jan 03, 2024)
2-28927666-A-G		not specified	Uncertain significance (Mar 01, 2023)
2-28929594-C-T		not specified	Uncertain significance (Jan 05, 2022)
2-28929595-G-A		not specified	Uncertain significance (Mar 01, 2024)
2-28929609-G-C		not specified	Uncertain significance (Oct 12, 2022)
2-28929663-G-A		not specified	Uncertain significance (Apr 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR43	protein_coding	protein_coding	ENST00000407426	18	53580

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000267	124587	0	14	124601	0.0000562

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.701	300	336	0.892	0.0000159	4378
Missense in Polyphen		51	98.635	0.51706		1285
Synonymous	-1.83	153	127	1.21	0.00000664	1238
Loss of Function	5.45	2	38.5	0.0519	0.00000186	504

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000142	0.000124
Ashkenazi Jewish	0.000409	0.000199
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000904	0.0000708
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000508	0.000331

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ribosome biogenesis factor. Involved in nucleolar processing of pre-18S ribosomal RNA. Required for optimal pre- ribosomal RNA transcription by RNA polymerase I. {ECO:0000269|PubMed:17699751}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Intolerance Scores

• rvis_EVS: -0.36
• rvis_percentile_EVS: 29.31

Haploinsufficiency Scores

• pHI: 0.422
• hipred: Y
• hipred_score: 0.711
• ghis: 0.598

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.420

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr43

Zebrafish Information Network

• Gene name: wdr43
• Affected structure: ventral wall of dorsal aorta
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: rRNA processing;positive regulation of transcription by RNA polymerase I;positive regulation of rRNA processing
• Cellular component: fibrillar center;nucleoplasm;nucleolus
• Molecular function: RNA binding;protein binding