ZZZ3

protein-coding

zinc finger ZZ-type containing 3, the group of ATAC complex|Zinc fingers ZZ-type|Myb/SANT domain containing

Gene summary

Enables histone binding activity. Involved in several processes, including regulation of cell division; regulation of transcription by RNA polymerase II; and regulation of tubulin deacetylation. Located in nucleolus and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_015534.6

Inheritance

—

ClinVar variants

U:110B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr1:77,562,416-77,683,419

External References & Databases

Ensembl (ENSG00000036549)

Transcript & Mutation Effects

hg38 • Region Span ~121.0 kb

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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 ZZZ3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 108

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015534.6. 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				1 clinvar	1 clinvar	2
missense			106 clinvar	4 clinvar		110
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	110	5	1	116

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 66 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015534.6	RefSeq	NP_056349.1	11	MANE Select
ENST00000370801.8	Ensembl	ENSP00000359837.3	11	MANE Select
NM_001308237.2	RefSeq	NP_001295166.1	11	Standard
NM_001376146.1	RefSeq	NP_001363075.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Chromatin modifying enzymes
HATs acetylate histones
Chromatin organization

Biological Process

regulation of transcription by RNA polymerase II

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
protein binding
zinc ion binding

Cellular Component

nucleus
Ada2/Gcn5/Ada3 transcription activator complex
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370801
Coding exons: 11
Length: 121004
Individuals with no LoFs: 125677
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125680
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.67	363	464	0.782	0.0000232	5959
Missense (PolyPhen)		89	155.9	0.57088		1923
Synonymous	1.19	139	158	0.879	0.00000766	1674
Loss of Function	5.71	3	43.8	0.0685	0.00000272	527

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000042	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0986

Intolerance Scores

LoFtool: 0.0474
RVIS EVS: -0.75
RVIS percentile EVS: 13.58

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 1.00

Gene Damage Prediction

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