DEPTOR

DEP domain containing MTOR interacting protein, the group of PDZ domain containing

Basic information

Region (hg38): 8:119873716-120050918

Previous symbols: [ "DEPDC6" ]

Links

ENSG00000155792 ∙ NCBI:64798 ∙ OMIM:612974 ∙ HGNC:22953 ∙ Uniprot:Q8TB45 ∙ 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 DEPTOR gene.

• Inborn genetic diseases (16 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEPTOR 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				1		1
missense			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	2	0

Variants in DEPTOR

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

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

Position	Type	Phenotype	Significance	ClinVar
8-119873851-A-T		not specified	Uncertain significance (Jun 26, 2023)
8-119873881-G-A		not specified	Uncertain significance (Feb 28, 2024)
8-119873908-G-A		not specified	Uncertain significance (Apr 25, 2023)
8-119873934-A-G		not specified	Uncertain significance (Oct 06, 2023)
8-119928440-C-T		not specified	Uncertain significance (Nov 08, 2022)
8-119928498-T-C		not specified	Uncertain significance (Feb 22, 2023)
8-119929860-G-A		not specified	Uncertain significance (Nov 09, 2021)
8-119929908-C-T		not specified	Uncertain significance (Mar 13, 2023)
8-119965281-G-T		not specified	Uncertain significance (Aug 22, 2023)
8-119965292-G-C		not specified	Uncertain significance (Feb 10, 2022)
8-119965351-C-A		not specified	Uncertain significance (Mar 07, 2024)
8-120001564-A-G		not specified	Uncertain significance (Dec 18, 2023)
8-120001614-A-G		not specified	Uncertain significance (Feb 12, 2024)
8-120001615-A-G		not specified	Likely benign (Jul 09, 2021)
8-120001687-G-A		not specified	Uncertain significance (Feb 15, 2023)
8-120002993-G-T		not specified	Uncertain significance (Dec 14, 2023)
8-120003003-G-T		not specified	Uncertain significance (Oct 03, 2023)
8-120003007-C-G		not specified	Uncertain significance (Apr 25, 2022)
8-120003051-T-C		not specified	Uncertain significance (Sep 07, 2022)
8-120003090-G-A		not specified	Uncertain significance (Jan 23, 2023)
8-120006845-C-T		not specified	Likely benign (Dec 15, 2023)
8-120009040-C-T			Likely benign (Feb 01, 2024)
8-120009042-C-T		not specified	Uncertain significance (Oct 29, 2021)
8-120009066-G-A		not specified	Conflicting classifications of pathogenicity (Mar 01, 2022)
8-120009119-G-A		not specified	Uncertain significance (Nov 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DEPTOR	protein_coding	protein_coding	ENST00000286234	9	177196

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.72e-12	0.0476	125675	0	73	125748	0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0875	245	249	0.984	0.0000142	2728
Missense in Polyphen		74	81.72	0.90553		870
Synonymous	0.460	87	92.6	0.939	0.00000537	751
Loss of Function	0.149	18	18.7	0.963	9.60e-7	215

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000734	0.000734
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000501	0.0000462
European (Non-Finnish)	0.000238	0.000237
Middle Eastern	0.000109	0.000109
South Asian	0.000592	0.000588
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negative regulator of the mTORC1 and mTORC2 signaling pathways. Inhibits the kinase activity of both complexes. {ECO:0000269|PubMed:19446321}.
• Pathway: mTOR signaling pathway - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);Steatosis AOP;Pathways in clear cell renal cell carcinoma;mTOR signaling pathway;Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met) (Consensus)

Intolerance Scores

• rvis_EVS: 0.07
• rvis_percentile_EVS: 58.96

Haploinsufficiency Scores

• pHI: 0.231
• hipred: Y
• hipred_score: 0.713
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Deptor

Gene ontology

• Biological process: negative regulation of protein kinase activity;negative regulation of TOR signaling;intracellular signal transduction;negative regulation of cell size;regulation of extrinsic apoptotic signaling pathway
• Molecular function: protein binding