DEPDC7

DEP domain containing 7

Basic information

Region (hg38): 11:33015876-33033582

Links

ENSG00000121690 ∙ NCBI:91614 ∙ OMIM:612294 ∙ HGNC:29899 ∙ Uniprot:Q96QD5 ∙ 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 DEPDC7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEPDC7 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						0
missense			12		1	13
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	1

Variants in DEPDC7

This is a list of pathogenic ClinVar variants found in the DEPDC7 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-33015972-A-C		not specified	Uncertain significance (Apr 23, 2024)
11-33015983-G-T		not specified	Uncertain significance (Oct 04, 2024)
11-33015992-C-T		not specified	Uncertain significance (Jun 24, 2022)
11-33016019-A-G		not specified	Uncertain significance (Mar 05, 2024)
11-33025665-G-A		not specified	Uncertain significance (Nov 18, 2022)
11-33025691-A-G		not specified	Uncertain significance (Mar 23, 2022)
11-33025904-G-A		not specified	Uncertain significance (Nov 02, 2023)
11-33025974-G-A		not specified	Uncertain significance (Jun 26, 2024)
11-33026036-T-C		not specified	Uncertain significance (Apr 01, 2024)
11-33027687-T-A		not specified	Uncertain significance (Oct 03, 2022)
11-33027775-C-T		not specified	Uncertain significance (Sep 04, 2024)
11-33027805-C-A		not specified	Uncertain significance (Apr 09, 2024)
11-33028606-T-C		not specified	Uncertain significance (Feb 05, 2024)
11-33028621-A-T		not specified	Uncertain significance (Apr 01, 2024)
11-33028758-G-C		not specified	Uncertain significance (Sep 02, 2024)
11-33028773-A-T			Uncertain significance (Jul 25, 2019)
11-33028779-T-A		not specified	Uncertain significance (Apr 20, 2024)
11-33028785-G-T		not specified	Uncertain significance (Jul 14, 2024)
11-33031444-A-T		not specified	Likely benign (Aug 27, 2024)
11-33031460-C-G		not specified	Uncertain significance (Dec 16, 2022)
11-33031494-A-G		not specified	Uncertain significance (Mar 15, 2024)
11-33031538-C-T		not specified	Uncertain significance (Jan 10, 2022)
11-33032443-G-A		not specified	Uncertain significance (Jul 06, 2022)
11-33032791-A-G		not specified	Uncertain significance (May 23, 2024)
11-33032957-T-G			Benign (Jun 15, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DEPDC7	protein_coding	protein_coding	ENST00000241051	9	17719

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.32e-11	0.455	124711	1	79	124791	0.000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.958	211	254	0.831	0.0000123	3353
Missense in Polyphen		56	64.852	0.86351		880
Synonymous	1.77	70	91.5	0.765	0.00000449	939
Loss of Function	1.17	19	25.4	0.749	0.00000157	309

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00127	0.00127
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.000334	0.000334
Finnish	0.00	0.00
European (Non-Finnish)	0.000306	0.000291
Middle Eastern	0.000334	0.000334
South Asian	0.000448	0.000392
Other	0.000371	0.000330

dbNSFP

Source: dbNSFP

• Pathway: Signal Transduction;Rho GTPase cycle;Signaling by Rho GTPases (Consensus)

Intolerance Scores

• loftool: 0.634
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.54

Haploinsufficiency Scores

• pHI: 0.0747
• hipred: N
• hipred_score: 0.291
• ghis: 0.443

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.683

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Depdc7

Gene ontology

• Biological process: biological_process;intracellular signal transduction;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction
• Cellular component: cellular_component;cytosol
• Molecular function: molecular_function;GTPase activator activity