DEPDC4

DEP domain containing 4

Basic information

Region (hg38): 12:100203669-100267079

Links

ENSG00000166153 ∙ NCBI:120863 ∙ ∙ HGNC:22952 ∙ Uniprot:Q8N2C3 ∙ 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 DEPDC4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEPDC4 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in DEPDC4

This is a list of pathogenic ClinVar variants found in the DEPDC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-100210112-C-T		not specified	Uncertain significance (Aug 02, 2021)
12-100212295-A-C		not specified	Uncertain significance (Jan 10, 2023)
12-100212470-C-G		not specified	Uncertain significance (Mar 31, 2023)
12-100212470-C-T		not specified	Uncertain significance (Feb 28, 2024)
12-100218493-G-A		not specified	Uncertain significance (Aug 17, 2022)
12-100218497-C-T		not specified	Uncertain significance (Apr 05, 2023)
12-100220016-C-G		not specified	Uncertain significance (Jan 02, 2024)
12-100220077-A-T		not specified	Uncertain significance (Oct 10, 2023)
12-100220079-C-T		not specified	Uncertain significance (Aug 02, 2021)
12-100220080-G-A		not specified	Uncertain significance (Nov 03, 2022)
12-100223786-C-A		not specified	Uncertain significance (Dec 13, 2022)
12-100262288-G-T		not specified	Uncertain significance (Jul 09, 2021)
12-100262353-A-G		not specified	Uncertain significance (Dec 27, 2023)
12-100262365-C-A		not specified	Uncertain significance (Dec 19, 2022)
12-100262377-G-A		not specified	Uncertain significance (May 23, 2023)
12-100263633-T-C		not specified	Uncertain significance (Oct 04, 2022)
12-100263637-C-A		not specified	Uncertain significance (Sep 17, 2021)
12-100263676-T-G		not specified	Uncertain significance (Aug 26, 2022)
12-100263696-T-C		not specified	Uncertain significance (May 22, 2023)
12-100263737-A-C		not specified	Uncertain significance (Jan 30, 2024)
12-100263789-T-C		not specified	Likely benign (Nov 19, 2022)
12-100263857-T-G		not specified	Uncertain significance (Nov 09, 2021)
12-100263882-G-T		not specified	Uncertain significance (Mar 31, 2024)
12-100266923-T-C		not specified	Uncertain significance (Nov 15, 2021)
12-100266992-G-A		not specified	Uncertain significance (Apr 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DEPDC4	protein_coding	protein_coding	ENST00000416321	5	63411

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.01e-9	0.0486	109272	0	8	109280	0.0000366

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.337	164	152	1.08	0.00000690	1952
Missense in Polyphen		40	32.946	1.2141		497
Synonymous	-0.333	58	54.9	1.06	0.00000264	542
Loss of Function	-0.390	13	11.6	1.12	4.86e-7	158

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000728	0.0000728
Ashkenazi Jewish	0.00	0.00
East Asian	0.000174	0.000174
Finnish	0.0000508	0.0000507
European (Non-Finnish)	0.0000196	0.0000196
Middle Eastern	0.000174	0.000174
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.801
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.16

Haploinsufficiency Scores

• pHI: 0.0975
• hipred: N
• hipred_score: 0.144
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.335

Gene Damage Prediction

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

Gene ontology

• Biological process: intracellular signal transduction