ZDBF2

protein-coding

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

Gene summary

This gene encodes a protein containing DBF4-type zinc finger domains. This gene is imprinted and paternally expressed in lymphocytes but is more stochastically expressed in the placenta. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2015]

MANE transcript

NM_020923.3

Inheritance

ClinVar variants

U:334B:131

Top phenotype

Nasopalpebral lipoma-coloboma syndrome

gnomAD constraint

pLI —, LoF o/e 0.28

Max pathogenic AF

—

Genomic locus

chr2:206,274,663-206,314,427

External References & Databases

Ensembl (ENSG00000204186)

Transcript & Mutation Effects

hg38 • Region Span ~39.8 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

schizophreniaNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0005090

Submitter: Labcorp Genetics (formerly Invitae)

nasopalpebral lipoma-coloboma syndromeLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0008182

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZDBF2 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 326

not providedTotal: 177

Nasopalpebral lipoma-coloboma syndromeTotal: 1

Breast ductal adenocarcinomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020923.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				36 clinvar	13 clinvar	49
missense			328 clinvar	60 clinvar	22 clinvar	410
nonsense			1 clinvar			1
start loss						0
frameshift			5 clinvar			5
splice donor/acceptor (+/-2bp)						0
Total	0	0	334	96	35	465

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 39 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020923.3	RefSeq	NP_065974.1	3	MANE Select
ENST00000374423.9	Ensembl	ENSP00000363545.3	3	MANE Select
NM_001285549.2	RefSeq	NP_001272478.1	3	Standard
NM_001369654.1	RefSeq	NP_001356583.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

nucleic acid binding
zinc ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374423
Coding exons: 3
Length: 39762
Individuals with no LoFs: 124590
Homozygous LoFs: 0
Heterozygous LoFs: 45
Defined: 124635
p: 0.000181

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.461	1140	1.18e+3	0.962	0.0000603	15701
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00019	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00029	0.00028	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0802

Intolerance Scores

LoFtool: 0.910
RVIS EVS: 1.8
RVIS percentile EVS: 96.93

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0442

Gene Damage Prediction

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