DEPDC1

DEP domain containing 1

Basic information

Region (hg38): 1:68474152-68497221

Links

ENSG00000024526 ∙ NCBI:55635 ∙ OMIM:612002 ∙ HGNC:22949 ∙ Uniprot:Q5TB30 ∙ 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 DEPDC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEPDC1 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			40	2	1	43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	2	2

Variants in DEPDC1

This is a list of pathogenic ClinVar variants found in the DEPDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-68476933-T-C			Benign (Jul 31, 2018)
1-68476940-G-T		not specified	Uncertain significance (Nov 07, 2024)
1-68476943-T-C		not specified	Uncertain significance (Jan 18, 2022)
1-68476945-C-A		not specified	Uncertain significance (Nov 30, 2022)
1-68476965-A-C		not specified	Uncertain significance (Sep 27, 2022)
1-68477038-T-C		not specified	Uncertain significance (Sep 25, 2023)
1-68477053-G-A		not specified	Uncertain significance (Dec 17, 2023)
1-68477810-C-T		not specified	Uncertain significance (Feb 11, 2022)
1-68477878-G-C		not specified	Uncertain significance (Oct 12, 2021)
1-68477944-G-A		not specified	Uncertain significance (Dec 21, 2023)
1-68477965-T-G		not specified	Uncertain significance (Nov 09, 2024)
1-68479187-T-C		not specified	Uncertain significance (Dec 16, 2023)
1-68479209-G-T		not specified	Uncertain significance (Jan 31, 2024)
1-68479230-T-C		not specified	Uncertain significance (Nov 24, 2024)
1-68479239-A-T		not specified	Uncertain significance (Sep 15, 2021)
1-68479283-G-A		not specified	Uncertain significance (Apr 12, 2023)
1-68479289-C-A		not specified	Uncertain significance (Feb 02, 2022)
1-68481450-G-A			Benign (Jul 31, 2018)
1-68481471-T-C		not specified	Uncertain significance (Nov 20, 2024)
1-68481476-C-T		not specified	Uncertain significance (Apr 17, 2023)
1-68481510-C-T		not specified	Uncertain significance (May 23, 2023)
1-68481511-G-A		not specified	Uncertain significance (Apr 09, 2024)
1-68481554-C-A		not specified	Uncertain significance (May 13, 2024)
1-68481597-T-A		not specified	Uncertain significance (Nov 24, 2024)
1-68482103-T-C		not specified	Uncertain significance (Dec 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DEPDC1	protein_coding	protein_coding	ENST00000456315	12	23070

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.64e-10	0.994	125687	0	61	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.443	377	402	0.938	0.0000192	5350
Missense in Polyphen		87	107.37	0.81029		1558
Synonymous	1.01	125	140	0.892	0.00000673	1480
Loss of Function	2.56	21	38.0	0.552	0.00000212	489

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000378	0.000377
Ashkenazi Jewish	0.000316	0.000298
East Asian	0.000964	0.000925
Finnish	0.00	0.00
European (Non-Finnish)	0.000224	0.000220
Middle Eastern	0.000964	0.000925
South Asian	0.0000984	0.0000980
Other	0.000519	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation as a transcriptional corepressor. The DEPDC1A-ZNF224 complex may play a critical role in bladder carcinogenesis by repressing the transcription of the A20 gene, leading to transport of NF-KB protein into the nucleus, resulting in suppression of apoptosis of bladder cancer cells. {ECO:0000269|PubMed:20587513}.

Recessive Scores

• pRec: 0.0847

Intolerance Scores

• loftool: 0.503
• rvis_EVS: -0.13
• rvis_percentile_EVS: 43.91

Haploinsufficiency Scores

• pHI: 0.0870
• hipred: N
• hipred_score: 0.492
• ghis: 0.615

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.134

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Depdc1a

Gene ontology

• Biological process: intracellular signal transduction;positive regulation of GTPase activity;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;transcriptional repressor complex
• Molecular function: GTPase activator activity;protein binding