DBF4

DBF4 zinc finger, the group of Zinc fingers DBF-type

Basic information

Region (hg38): 7:87876215-87909553

Links

ENSG00000006634 ∙ NCBI:10926 ∙ OMIM:604281 ∙ HGNC:17364 ∙ Uniprot:Q9UBU7 ∙ 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 DBF4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DBF4 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			24		2	26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	3

Variants in DBF4

This is a list of pathogenic ClinVar variants found in the DBF4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-87878060-C-A			Benign (May 21, 2018)
7-87878082-A-G		not specified	Uncertain significance (Aug 22, 2023)
7-87878147-G-C		not specified	Uncertain significance (Jul 06, 2022)
7-87896493-G-A		not specified	Uncertain significance (Jan 24, 2024)
7-87900302-T-G		not specified	Uncertain significance (Nov 12, 2021)
7-87900307-A-T		not specified	Uncertain significance (Jun 06, 2023)
7-87904317-A-G		not specified	Uncertain significance (Oct 05, 2023)
7-87907210-C-T		not specified	Uncertain significance (Jun 02, 2023)
7-87907241-A-G		not specified	Uncertain significance (Dec 27, 2022)
7-87907300-G-C		not specified	Uncertain significance (Aug 28, 2023)
7-87907388-C-G		not specified	Uncertain significance (Aug 14, 2023)
7-87907390-C-G		not specified	Uncertain significance (Feb 26, 2024)
7-87907454-C-T		not specified	Uncertain significance (May 31, 2023)
7-87907694-A-C		not specified	Uncertain significance (Aug 17, 2022)
7-87907714-A-G			Benign (Jan 12, 2018)
7-87907721-C-T		not specified	Uncertain significance (Dec 14, 2022)
7-87907723-C-T		not specified	Uncertain significance (Nov 14, 2023)
7-87907740-A-G		not specified	Uncertain significance (Jun 06, 2023)
7-87907756-C-A		not specified	Uncertain significance (Dec 01, 2023)
7-87907796-C-T		not specified	Uncertain significance (Aug 21, 2023)
7-87907810-C-T		not specified	Uncertain significance (Nov 10, 2022)
7-87907865-G-A		not specified	Uncertain significance (Jan 17, 2024)
7-87907873-A-G			Benign (Jan 12, 2018)
7-87907961-A-G		not specified	Uncertain significance (Nov 21, 2023)
7-87908033-T-G		not specified	Uncertain significance (Mar 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DBF4	protein_coding	protein_coding	ENST00000265728	12	33326

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00704	125724	0	18	125742	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.979	274	324	0.847	0.0000145	4467
Missense in Polyphen		38	62.081	0.6121		936
Synonymous	0.147	113	115	0.983	0.00000543	1182
Loss of Function	4.63	4	32.4	0.123	0.00000161	450

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000888	0.0000888
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000332	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulatory subunit for CDC7 which activates its kinase activity thereby playing a central role in DNA replication and cell proliferation. Required for progression of S phase. The complex CDC7-DBF4A selectively phosphorylates MCM2 subunit at 'Ser-40' and 'Ser-53' and then is involved in regulating the initiation of DNA replication during cell cycle. {ECO:0000269|PubMed:10373557, ECO:0000269|PubMed:10523313, ECO:0000269|PubMed:17062569}.
• Pathway: Cell cycle - Homo sapiens (human);Cell Cycle;DNA Replication;Activation of ATR in response to replication stress;G2/M Checkpoints;Cell Cycle Checkpoints;Activation of the pre-replicative complex;Mitotic G1-G1/S phases;DNA Replication;G1/S Transition;DNA Replication Pre-Initiation;M/G1 Transition;Cell Cycle;Cell Cycle, Mitotic (Consensus)

Recessive Scores

• pRec: 0.152

Intolerance Scores

• loftool: 0.437
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.74

Haploinsufficiency Scores

• pHI: 0.346
• hipred: Y
• hipred_score: 0.746
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.707

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dbf4
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: G1/S transition of mitotic cell cycle;DNA replication;positive regulation of DNA replication;positive regulation of protein serine/threonine kinase activity
• Cellular component: nucleus;nucleoplasm;nuclear body;Dbf4-dependent protein kinase complex
• Molecular function: nucleic acid binding;protein binding;enzyme activator activity;zinc ion binding;protein kinase binding;protein serine/threonine kinase activator activity