ZDBF2

zinc finger DBF-type containing 2, the group of Zinc fingers DBF-type

Basic information

Region (hg38): 2:206274663-206314427

Links

ENSG00000204186 ∙ NCBI:57683 ∙ OMIM:617059 ∙ HGNC:29313 ∙ Uniprot:Q9HCK1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown
• nasopalpebral lipoma-coloboma syndrome (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZDBF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZDBF2 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				24	14	38
missense			178	38	21	237
nonsense			1			1
start loss						0
frameshift			2			2
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	182	62	36

Variants in ZDBF2

This is a list of pathogenic ClinVar variants found in the ZDBF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-206281883-C-T		not specified	Likely benign (Sep 30, 2024)
2-206281916-G-A			Benign (Oct 23, 2024)
2-206297257-T-C			Likely benign (May 26, 2023)
2-206297282-C-G		not specified	Uncertain significance (Aug 02, 2021)
2-206297292-G-A		not specified	Uncertain significance (Oct 07, 2024)
2-206297297-A-G		not specified	Uncertain significance (Jun 25, 2024)
2-206297300-T-C		not specified	Uncertain significance (Jun 02, 2023)
2-206297301-G-T		not specified	Uncertain significance (Dec 19, 2022)
2-206297303-A-G		not specified	Uncertain significance (May 05, 2022)
2-206297309-A-G			Benign (Jan 29, 2025)
2-206297369-A-G		not specified	Uncertain significance (Oct 06, 2023)
2-206297370-G-C		not specified	Uncertain significance (Jan 14, 2025)
2-206297372-A-G		not specified	Uncertain significance (Oct 25, 2024)
2-206304700-C-T			Benign (Oct 23, 2024)
2-206304762-A-G			Benign (Dec 02, 2024)
2-206304824-A-T			Benign (Oct 17, 2024)
2-206304833-C-G		not specified	Uncertain significance (Sep 14, 2022)
2-206304838-G-A			Uncertain significance (Jan 31, 2023)
2-206304852-C-T			Likely benign (Oct 04, 2023)
2-206304875-A-T		not specified	Uncertain significance (Nov 22, 2023)
2-206304878-T-G			Uncertain significance (Sep 18, 2024)
2-206304911-C-T		not specified	Uncertain significance (Apr 25, 2023)
2-206304912-G-A			Likely benign (Dec 11, 2023)
2-206304914-A-G			Likely benign (Nov 18, 2024)
2-206304925-G-A		not specified	Likely benign (Oct 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZDBF2	protein_coding	protein_coding	ENST00000374423	3	39762

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0103	0.990	124590	0	45	124635	0.000181

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.461	1140	1.18e+3	0.962	0.0000603	15701
Missense in Polyphen		62	68.509	0.905		880
Synonymous	0.413	412	423	0.974	0.0000215	4358
Loss of Function	4.31	12	42.3	0.284	0.00000193	630

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000252	0.000252
Ashkenazi Jewish	0.000200	0.000199
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000285	0.000283
Middle Eastern	0.000111	0.000111
South Asian	0.000132	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0802

Intolerance Scores

• loftool: 0.910
• rvis_EVS: 1.8
• rvis_percentile_EVS: 96.93

Haploinsufficiency Scores

• pHI: 0.0949
• hipred: N
• hipred_score: 0.324
• ghis: 0.451

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0442

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zdbf2
• Phenotype: cellular phenotype; growth/size/body region phenotype

Gene ontology

• Molecular function: nucleic acid binding;zinc ion binding