WDR59

WD repeat domain 59, the group of GATOR2 subcomplex|WD repeat domain containing

Basic information

Region (hg38): 16:74871361-75000173

Links

ENSG00000103091 ∙ NCBI:79726 ∙ OMIM:617418 ∙ HGNC:25706 ∙ Uniprot:Q6PJI9 ∙ 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 WDR59 gene.

• Inborn genetic diseases (41 variants)
• not provided (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the WDR59 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				4	3	7
missense			40	1	4	45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	40	5	7

Variants in WDR59

This is a list of pathogenic ClinVar variants found in the WDR59 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-74874248-G-A			Benign (May 21, 2018)
16-74874315-G-T		not specified	Uncertain significance (Apr 12, 2022)
16-74874328-T-C		not specified	Uncertain significance (Mar 07, 2024)
16-74874333-G-A		not specified	Uncertain significance (Feb 14, 2023)
16-74874387-A-G		not specified	Uncertain significance (Feb 27, 2024)
16-74874399-G-A		not specified	Uncertain significance (May 24, 2023)
16-74874417-C-T		not specified	Uncertain significance (Aug 30, 2022)
16-74885659-C-G		not specified	Uncertain significance (May 05, 2023)
16-74885677-G-A		not specified	Uncertain significance (Dec 21, 2023)
16-74886307-G-A		not specified	Uncertain significance (Sep 16, 2021)
16-74887695-C-A			Benign (Dec 31, 2019)
16-74888203-C-T		not specified	Uncertain significance (May 25, 2022)
16-74888204-G-A		not specified	Uncertain significance (Dec 08, 2023)
16-74888208-A-G			Benign (May 21, 2018)
16-74888296-C-T		not specified	Uncertain significance (Dec 22, 2023)
16-74888297-G-A		not specified	Uncertain significance (Oct 07, 2022)
16-74888302-C-T		not specified	Likely benign (Nov 08, 2022)
16-74888308-T-C		not specified	Uncertain significance (Sep 20, 2023)
16-74889799-G-A		not specified	Uncertain significance (Feb 21, 2024)
16-74889808-G-A		not specified	Uncertain significance (Feb 16, 2023)
16-74892508-G-A			Likely benign (Feb 01, 2023)
16-74893697-G-A		not specified	Uncertain significance (Feb 15, 2023)
16-74893702-G-C		not specified	Uncertain significance (Dec 14, 2023)
16-74893737-T-C		not specified	Uncertain significance (Oct 25, 2022)
16-74893763-C-T		not specified	Uncertain significance (Dec 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
WDR59	protein_coding	protein_coding	ENST00000262144	26	126604

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.06e-14	1.00	125656	0	91	125747	0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	503	588	0.855	0.0000356	6374
Missense in Polyphen		118	161.26	0.73176		1715
Synonymous	-3.66	291	222	1.31	0.0000133	1863
Loss of Function	3.30	32	59.4	0.538	0.00000319	624

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000727	0.000726
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000324	0.000323
European (Non-Finnish)	0.000519	0.000492
Middle Eastern	0.000163	0.000163
South Asian	0.000201	0.000196
Other	0.000331	0.000326

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. 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:25457612, PubMed:27487210). {ECO:0000269|PubMed:23723238, ECO:0000269|PubMed:25457612, ECO:0000269|PubMed:27487210}.
• Pathway: mTOR signaling pathway - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.784
• rvis_EVS: -1.26
• rvis_percentile_EVS: 5.34

Haploinsufficiency Scores

• pHI: 0.220
• hipred: Y
• hipred_score: 0.554
• ghis: 0.608

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.806

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Wdr59
• Phenotype: limbs/digits/tail phenotype; 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); embryo phenotype; growth/size/body region phenotype

Gene ontology

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