ZZEF1

protein-coding

zinc finger ZZ-type and EF-hand domain containing 1, the group of Zinc fingers ZZ-type|EF-hand domain containing

Gene summary

Enables histone binding activity. Predicted to be involved in DNA-templated transcription. Predicted to act upstream of or within several processes, including glutamatergic synaptic transmission; regulation of peptidyl-tyrosine phosphorylation; and visual learning. Predicted to be located in cell surface; postsynapse; and presynaptic active zone. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_015113.4

Inheritance

—

ClinVar variants

U:462B:29

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr17:4,004,445-4,143,030

External References & Databases

Ensembl (ENSG00000074755)

Transcript & Mutation Effects

hg38 • Region Span ~138.6 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZZEF1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 449

not providedTotal: 10

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015113.4. 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			8 clinvar	6 clinvar		14
missense			443 clinvar	22 clinvar		465
nonsense				1 clinvar		1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			10 clinvar			10
Total	0	0	462	29	0	491

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015113.4	RefSeq	NP_055928.3	55	MANE Select
ENST00000381638.7	Ensembl	ENSP00000371051.2	55	MANE Select
ENST00000571436.5	Ensembl	ENSP00000459023.1	5	Standard
ENST00000572699.1	Ensembl	ENSP00000460633.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

calcium ion binding
zinc ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000381638
Coding exons: 55
Length: 138576
Individuals with no LoFs: 125691
Homozygous LoFs: 0
Heterozygous LoFs: 57
Defined: 125748
p: 0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.05	1534	1.65e+3	0.928	0.0000954	19343
Missense (PolyPhen)		459	608.09	0.75482		7365
Synonymous	-1.29	703	661	1.06	0.0000401	5783
Loss of Function	8.92	33	151	0.218	0.00000786	1738

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00011	0.00011	rare
Finnish	0.00020	0.00018	rare
European (Non-Finnish)	0.00026	0.00025	rare
South Asian	0.00029	0.00029	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.103

Intolerance Scores

LoFtool: 0.550
RVIS EVS: -3.38
RVIS percentile EVS: 0.39

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.708

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High