DEPDC1B

DEP domain containing 1B

Basic information

Region (hg38): 5:60596912-60700190

Links

ENSG00000035499 ∙ NCBI:55789 ∙ OMIM:616073 ∙ HGNC:24902 ∙ Uniprot:Q8WUY9 ∙ 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 DEPDC1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEPDC1B 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			47			47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	1	0

Variants in DEPDC1B

This is a list of pathogenic ClinVar variants found in the DEPDC1B region.

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

Position	Type	Phenotype	Significance	ClinVar
5-60597787-T-A		not specified	Uncertain significance (Dec 03, 2021)
5-60597829-G-A		not specified	Uncertain significance (Oct 30, 2024)
5-60597880-C-T		not specified	Uncertain significance (Dec 04, 2024)
5-60599142-G-A		not specified	Uncertain significance (Feb 06, 2025)
5-60599145-G-T		not specified	Uncertain significance (Jan 24, 2025)
5-60599166-T-C		not specified	Uncertain significance (Aug 19, 2023)
5-60599197-T-C		not specified	Uncertain significance (Jun 25, 2024)
5-60599205-C-T		not specified	Uncertain significance (Feb 28, 2023)
5-60599206-G-A		not specified	Uncertain significance (Mar 29, 2022)
5-60599233-T-C		not specified	Uncertain significance (Apr 25, 2022)
5-60603416-C-T		not specified	Uncertain significance (Sep 20, 2023)
5-60603431-G-T		not specified	Uncertain significance (Oct 28, 2023)
5-60603522-C-T		not specified	Uncertain significance (Jun 29, 2023)
5-60603548-C-T		not specified	Uncertain significance (Mar 01, 2025)
5-60603558-T-A		not specified	Uncertain significance (Dec 24, 2024)
5-60605697-C-T		not specified	Uncertain significance (May 18, 2022)
5-60605700-G-A		not specified	Uncertain significance (Nov 14, 2024)
5-60605763-A-G		not specified	Uncertain significance (Jul 27, 2024)
5-60605784-C-T		not specified	Uncertain significance (Sep 29, 2022)
5-60605833-C-A		not specified	Uncertain significance (Aug 04, 2023)
5-60638860-A-G		not specified	Uncertain significance (May 17, 2023)
5-60638864-G-C		not specified	Uncertain significance (Oct 25, 2024)
5-60638884-T-C		not specified	Uncertain significance (Dec 14, 2023)
5-60644753-T-C		not specified	Uncertain significance (Jan 06, 2023)
5-60644754-C-T		not specified	Uncertain significance (Mar 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DEPDC1B	protein_coding	protein_coding	ENST00000265036	11	103279

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.42e-10	0.803	125694	0	52	125746	0.000207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.852	245	285	0.858	0.0000155	3459
Missense in Polyphen		75	83.885	0.89408		958
Synonymous	-0.347	106	102	1.04	0.00000532	978
Loss of Function	1.62	19	28.3	0.671	0.00000147	355

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000147	0.000147
Ashkenazi Jewish	0.00	0.00
East Asian	0.000280	0.000272
Finnish	0.000142	0.000139
European (Non-Finnish)	0.000242	0.000237
Middle Eastern	0.000280	0.000272
South Asian	0.000402	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.479
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.91

Haploinsufficiency Scores

• pHI: 0.785
• hipred: N
• hipred_score: 0.348
• ghis: 0.692

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.215

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Depdc1b

Gene ontology

• Biological process: cell migration;positive regulation of Wnt signaling pathway;intracellular signal transduction;positive regulation of GTPase activity;regulation of small GTPase mediated signal transduction
• Cellular component: cytosol
• Molecular function: GTPase activator activity