WDR24

WD repeat domain 24, the group of WD repeat domain containing|GATOR2 subcomplex

Basic information

Region (hg38): 16:684622-690444

Previous symbols: [ "C16orf21" ]

Links

ENSG00000127580 ∙ NCBI:84219 ∙ OMIM:620307 ∙ HGNC:20852 ∙ Uniprot:Q96S15 ∙ 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 WDR24 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR24 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			33	2		35
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	34	3	0

Variants in WDR24

This is a list of pathogenic ClinVar variants found in the WDR24 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-684799-T-A		not specified	Uncertain significance (Jan 23, 2024)
16-684894-C-A		not specified	Uncertain significance (Jan 03, 2024)
16-685070-T-A		not specified	Uncertain significance (Dec 05, 2022)
16-685164-T-A		not specified	Uncertain significance (Mar 07, 2023)
16-685292-C-T		not specified	Uncertain significance (Jul 05, 2023)
16-685357-A-G		not specified	Uncertain significance (Aug 10, 2023)
16-685426-A-G		not specified	Uncertain significance (Mar 28, 2024)
16-685448-C-T		not specified	Uncertain significance (Jun 05, 2024)
16-685459-G-A		not specified	Uncertain significance (Sep 23, 2023)
16-685472-C-T		not specified	Uncertain significance (Sep 21, 2021)
16-685480-C-T		not specified	Uncertain significance (Feb 23, 2023)
16-685487-C-T		not specified	Uncertain significance (Aug 21, 2023)
16-685513-A-G		not specified	Uncertain significance (Jan 18, 2023)
16-685544-T-A		not specified	Uncertain significance (May 17, 2023)
16-685729-ACG-A			Uncertain significance (Sep 05, 2023)
16-685892-G-A		not specified	Uncertain significance (Jun 17, 2022)
16-685899-C-T		not specified	Uncertain significance (Mar 24, 2023)
16-685985-T-A		not specified	Uncertain significance (Feb 12, 2024)
16-686092-G-A		not specified	Uncertain significance (Jul 26, 2022)
16-686120-G-A		not specified	Uncertain significance (Oct 20, 2021)
16-686186-C-T			Uncertain significance (Sep 05, 2023)
16-686817-G-A		not specified	Uncertain significance (Dec 07, 2021)
16-686860-C-T		not specified	Likely benign (Aug 11, 2022)
16-686871-G-A		not specified	Likely benign (Nov 08, 2022)
16-686883-C-T		not specified	Uncertain significance (May 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR24	protein_coding	protein_coding	ENST00000293883	9	5823

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000235	0.999	125662	0	21	125683	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.79	378	565	0.669	0.0000411	5177
Missense in Polyphen		84	216.6	0.38781		1992
Synonymous	-3.40	319	251	1.27	0.0000208	1582
Loss of Function	2.92	13	30.4	0.428	0.00000156	295

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000248	0.000246
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000126	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As a component of the GATOR subcomplex GATOR2, functions within the amino acid-sensing branch of the TORC1 signaling pathway (PubMed:23723238, PubMed:27166823). Indirectly activates mTORC1 and the TORC1 signaling pathway through the inhibition of the GATOR1 subcomplex (PubMed:23723238). It is negatively regulated by the upstream amino acid sensors SESN2 and CASTOR1 (PubMed:26449471, PubMed:26586190, PubMed:27487210). In addition to its role in regulation of the TORC1 complex, promotes the acidification of lysosomes and facilitates autophagic flux (PubMed:27166823). {ECO:0000269|PubMed:23723238, ECO:0000269|PubMed:26449471, ECO:0000269|PubMed:26586190, ECO:0000269|PubMed:27166823, ECO:0000269|PubMed:27487210}.
• Pathway: mTOR signaling pathway - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.466
• rvis_EVS: -0.46
• rvis_percentile_EVS: 23.66

Haploinsufficiency Scores

• pHI: 0.171
• hipred: Y
• hipred_score: 0.575
• ghis: 0.562

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.868

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr24

Gene ontology

• Biological process: autophagy;regulation of autophagy;positive regulation of TOR signaling;cellular response to amino acid starvation
• Cellular component: lysosomal membrane;GATOR2 complex
• Molecular function: protein binding