WDR12

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

Basic information

Region (hg38): 2:202874261-203014798

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.

not_specified (50 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. These statistics are base on transcript: NM_000018256.4. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			48 clinvar	2 clinvar		50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	48	2	0

Loading clinvar variants...

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