DBF4B

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

Basic information

Region (hg38): 17:44708608-44752264

Links

ENSG00000161692 ∙ NCBI:80174 ∙ OMIM:611661 ∙ HGNC:17883 ∙ Uniprot:Q8NFT6 ∙ 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 DBF4B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DBF4B 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			34	5		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	5	0

Variants in DBF4B

This is a list of pathogenic ClinVar variants found in the DBF4B region.

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

Position	Type	Phenotype	Significance	ClinVar
17-44709330-T-C		not specified	Uncertain significance (Jul 14, 2021)
17-44709333-A-G		not specified	Uncertain significance (Mar 20, 2023)
17-44709339-G-C		not specified	Uncertain significance (Nov 25, 2024)
17-44709358-C-G		not specified	Uncertain significance (Jan 19, 2025)
17-44722892-G-A		not specified	Likely benign (Feb 17, 2022)
17-44723002-G-A		not specified	Uncertain significance (Dec 13, 2023)
17-44729921-T-C		not specified	Uncertain significance (Nov 16, 2022)
17-44729927-A-G		not specified	Uncertain significance (Feb 13, 2025)
17-44729932-G-A		not specified	Uncertain significance (Aug 02, 2023)
17-44729944-G-A		not specified	Uncertain significance (Dec 14, 2021)
17-44730072-G-T		not specified	Uncertain significance (Apr 25, 2023)
17-44730088-G-A		not specified	Likely benign (Nov 25, 2024)
17-44730975-G-A		not specified	Uncertain significance (Mar 03, 2025)
17-44732212-G-A		not specified	Uncertain significance (Oct 13, 2023)
17-44732242-G-T		not specified	Uncertain significance (Feb 26, 2025)
17-44732259-G-A		not specified	Uncertain significance (Jan 10, 2025)
17-44734093-T-C		not specified	Uncertain significance (Oct 13, 2023)
17-44734104-G-A		not specified	Likely benign (Sep 16, 2021)
17-44734123-C-T		not specified	Uncertain significance (Sep 16, 2021)
17-44736840-C-T		not specified	Uncertain significance (Sep 17, 2021)
17-44736860-C-T		not specified	Uncertain significance (Aug 19, 2024)
17-44736861-G-A		not specified	Uncertain significance (Dec 03, 2024)
17-44741425-C-T		not specified	Uncertain significance (Oct 14, 2023)
17-44747139-G-A		not specified	Uncertain significance (Jan 01, 2025)
17-44747413-G-A		not specified	Likely benign (Jun 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DBF4B	protein_coding	protein_coding	ENST00000315005	14	43657

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.68e-11	0.264	125698	0	50	125748	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.855	306	351	0.872	0.0000191	3993
Missense in Polyphen		49	64.536	0.75927		765
Synonymous	0.649	127	137	0.929	0.00000778	1239
Loss of Function	0.912	19	23.8	0.798	0.00000111	280

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000329	0.000329
Ashkenazi Jewish	0.00	0.00
East Asian	0.000547	0.000544
Finnish	0.000187	0.000185
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.000547	0.000544
South Asian	0.000229	0.000229
Other	0.000654	0.000652

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 and M phases. The complex CDC7-DBF4B selectively phosphorylates MCM2 subunit at 'Ser-40' and then is involved in regulating the initiation of DNA replication during cell cycle. {ECO:0000269|PubMed:12065429, ECO:0000269|PubMed:15668232, ECO:0000269|PubMed:17062569}.

Intolerance Scores

• loftool: 0.986
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.51

Haploinsufficiency Scores

• pHI: 0.115
• hipred: N
• hipred_score: 0.438
• ghis: 0.483

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.245

Gene Damage Prediction

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

Gene ontology

• Biological process: cell cycle;positive regulation of cell population proliferation;positive regulation of nuclear cell cycle DNA replication;positive regulation of G2/M transition of mitotic cell cycle;activation of protein kinase activity;positive regulation of DNA replication;positive regulation of protein serine/threonine kinase activity
• Cellular component: nuclear chromatin;nucleus;nucleoplasm;cytoplasm;aggresome;Dbf4-dependent protein kinase complex;intracellular membrane-bounded organelle
• Molecular function: nucleic acid binding;protein binding;zinc ion binding;protein kinase binding;protein kinase activator activity;protein serine/threonine kinase activator activity