WDR12

WD repeat domain 12, the group of WD repeat domain containing|PeBoW complex

Basic information

Region (hg38): 2:202874260-203014798

Links

ENSG00000138442 ∙ NCBI:55759 ∙ OMIM:616620 ∙ HGNC:14098 ∙ Uniprot:Q9GZL7 ∙ 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 WDR12 gene.

• Inborn genetic diseases (17 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR12 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			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in WDR12

This is a list of pathogenic ClinVar variants found in the WDR12 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-202880905-C-A		not specified	Uncertain significance (Jun 24, 2022)
2-202882715-G-C		not specified	Uncertain significance (Aug 30, 2022)
2-202882776-C-G		not specified	Uncertain significance (Nov 21, 2022)
2-202883675-G-A		not specified	Uncertain significance (Dec 16, 2023)
2-202883726-G-A		not specified	Uncertain significance (Nov 20, 2023)
2-202884242-C-G		not specified	Uncertain significance (Feb 05, 2024)
2-202884254-C-T		not specified	Uncertain significance (Dec 19, 2022)
2-202884272-T-C		not specified	Uncertain significance (Feb 08, 2023)
2-202884414-C-T		not specified	Uncertain significance (Oct 12, 2021)
2-202884435-C-T		not specified	Uncertain significance (Feb 15, 2023)
2-202892664-T-C		not specified	Uncertain significance (Oct 25, 2023)
2-202892690-T-A		not specified	Uncertain significance (Feb 23, 2023)
2-202894616-C-G		not specified	Uncertain significance (Mar 01, 2024)
2-202896100-C-T		not specified	Uncertain significance (Aug 02, 2023)
2-202897324-T-C		not specified	Uncertain significance (May 23, 2023)
2-202897332-T-C		not specified	Uncertain significance (Oct 06, 2022)
2-202897333-C-T		not specified	Uncertain significance (Mar 17, 2023)
2-202897348-T-C		not specified	Uncertain significance (Sep 21, 2023)
2-202897366-C-T		not specified	Uncertain significance (Sep 14, 2023)
2-202897384-G-A		not specified	Uncertain significance (Aug 18, 2021)
2-202897405-C-T		not specified	Uncertain significance (Nov 27, 2023)
2-202907901-T-C		not specified	Uncertain significance (Apr 21, 2022)
2-202907952-C-T		not specified	Likely benign (Feb 10, 2022)
2-202911449-T-C		not specified	Uncertain significance (May 26, 2023)
2-202941934-A-C		not specified	Uncertain significance (Dec 13, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR12	protein_coding	protein_coding	ENST00000261015	13	140017

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000326	0.999	125725	0	21	125746	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.476	199	219	0.909	0.0000104	2763
Missense in Polyphen		56	71.59	0.78223		944
Synonymous	0.407	75	79.6	0.942	0.00000397	788
Loss of Function	3.05	11	28.6	0.385	0.00000145	327

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000302	0.000301
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.000163	0.000163
South Asian	0.0000661	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the PeBoW complex, which is required for maturation of 28S and 5.8S ribosomal RNAs and formation of the 60S ribosome. {ECO:0000255|HAMAP-Rule:MF_03029, ECO:0000269|PubMed:16043514, ECO:0000269|PubMed:17353269}.

Intolerance Scores

• loftool: 0.662
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.6

Haploinsufficiency Scores

• pHI: 0.688
• hipred: Y
• hipred_score: 0.696
• ghis: 0.652

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr12
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); pigmentation phenotype

Zebrafish Information Network

• Gene name: wdr12
• Affected structure: anatomical system
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);rRNA processing;Notch signaling pathway;cell population proliferation;ribosomal large subunit biogenesis
• Cellular component: nucleoplasm;nucleolus;preribosome, large subunit precursor;PeBoW complex
• Molecular function: protein binding;ribonucleoprotein complex binding