ZFP64

protein-coding

ZFP64 zinc finger protein, the group of Zinc fingers C2H2-type

Gene summary

Predicted to enable DNA-binding transcription factor activity and transcription cis-regulatory region binding activity. Involved in mesenchymal cell differentiation. Located in cytoplasm and megasporocyte nucleus. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ZNF338

MANE transcript

NM_018197.3

Inheritance

—

ClinVar variants

U:85B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr20:52,051,663-52,204,308

External References & Databases

Ensembl (ENSG00000020256)

Transcript & Mutation Effects

hg38 • Region Span ~152.6 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 ZFP64 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 85

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018197.3. 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						0
missense			85 clinvar	2 clinvar		87
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	85	2	0	87

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 42 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018197.3	RefSeq	NP_060667.2	6	MANE Select
ENST00000216923.5	Ensembl	ENSP00000216923.4	6	MANE Select
NM_001319146.2	RefSeq	NP_001306075.1	5	Standard
NM_022088.5	RefSeq	NP_071371.3	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
regulation of gene expression

Molecular Function

RNA polymerase II core promoter sequence-specific DNA binding
DNA-binding transcription factor activity, RNA polymerase II-specific
DNA binding
protein binding
metal ion binding

Cellular Component

nucleus
histone methyltransferase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000216923
Coding exons: 6
Length: 152646
Individuals with no LoFs: 125733
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 125748
p: 0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.94	315	428	0.736	0.0000278	4507
Missense (PolyPhen)		112	194.18	0.57679		2227
Synonymous	-0.118	185	183	1.01	0.0000135	1324
Loss of Function	2.42	10	22.4	0.447	0.00000105	258

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.00016	0.00014	rare
European (Non-Finnish)	0.000053	0.000053	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation.;

Recessive Scores

pRec: 0.116

Intolerance Scores

LoFtool: 0.420
RVIS EVS: 0.45
RVIS percentile EVS: 78.04

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.880

Gene Damage Prediction

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