WDR24

protein-coding

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

Gene summary

Enables ubiquitin protein ligase activity. Involved in several processes, including cellular response to amino acid starvation; positive regulation of TORC1 signaling; and protein K6-linked ubiquitination. Acts upstream of or within protein localization to plasma membrane. Located in lysosomal membrane. Part of GATOR2 complex. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C16orf21

MANE transcript

NM_032259.4

Inheritance

—

ClinVar variants

U:111B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.43

Max pathogenic AF

—

Genomic locus

chr16:684,622-690,444

External References & Databases

Ensembl (ENSG00000127580)

Transcript & Mutation Effects

hg38 • Region Span ~5.8 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to WDR24 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 111

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032259.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	2 clinvar		4
missense			108 clinvar	4 clinvar		112
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	111	6	0	117

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032259.4	RefSeq	NP_115635.1	9	MANE Select
ENST00000293883.9	Ensembl	ENSP00000293883.4	9	MANE Select
ENST00000248142.7	Ensembl	ENSP00000248142.6	13	Standard
ENST00000647644.1	Ensembl	ENSP00000497264.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

mTOR signaling pathway - Homo sapiens (human)

Biological Process

autophagy
regulation of autophagy
positive regulation of TOR signaling
cellular response to amino acid starvation

Molecular Function

protein binding

Cellular Component

lysosomal membrane
GATOR2 complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000293883
Coding exons: 9
Length: 5823
Individuals with no LoFs: 125662
Homozygous LoFs: 0
Heterozygous LoFs: 21
Defined: 125683
p: 0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.79	378	565	0.669	0.0000411	5177
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00013	0.00012	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.107

Intolerance Scores

LoFtool: 0.466
RVIS EVS: -0.46
RVIS percentile EVS: 23.66

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.868

Gene Damage Prediction

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