GeneBe

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.

  • not_specified (98 variants)
  • not_provided (3 variants)

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. These statistics are base on transcript: NM_000032259.4. 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
 2
missense
94
clinvar
4
clinvar
 98
nonsense
0
start loss
0
frameshift
1
clinvar
 1
splice donor/acceptor (+/-2bp)
0
Total 0 0 95 6 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
WDR24protein_codingprotein_codingENST00000293883 95823
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.00002350.9991256620211256830.0000835
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.793785650.6690.00004115177
Missense in Polyphen84216.60.387811992
Synonymous-3.403192511.270.00002081582
Loss of Function2.921330.40.4280.00000156295

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002480.000246
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.0001260.000123
Middle Eastern0.00005440.0000544
South Asian0.00006540.0000653
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Wdr24
Phenotype

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