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

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 26.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_020923.3	NP_065974.1	3	yes	-
ENST00000374423.9	ENSP00000363545.3	3	yes	-
NM_001285549.2	NP_001272478.1	3	-	-
NM_001369654.1	NP_001356583.1	3	-	-

Phenotypes

GenCC

Source: genCC

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

ClinVar

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

• not_specified (326 variants)
• not_provided (176 variants)
• Nasopalpebral_lipoma-coloboma_syndrome (1 variants)
• Breast_ductal_adenocarcinoma (1 variants)

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. These statistics are base on transcript: NM_020923.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				36	13	49
missense			327	60	22	409
nonsense			1			1
start loss						0
frameshift			5			5
splice donor/acceptor (+/-2bp)						0
Total	0	0	333	96	35

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
		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

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

Gene ontology

• Molecular function: nucleic acid binding;zinc ion binding