ZNF66

protein-coding

zinc finger protein 66, the group of Zinc fingers C2H2-type

Gene summary

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of DNA-templated transcription. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

ZNF66P

MANE transcript

NM_001355197.2

Inheritance

—

ClinVar variants

B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr19:20,776,304-20,809,995

External References & Databases

Ensembl (ENSG00000160229)

Transcript & Mutation Effects

hg38 • Region Span ~33.7 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 ZNF66 variants in ClinVar

1 Conditions Cataloged

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001355197.2. 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				4 clinvar		4
missense						0
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	0	4	0	4

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001355197.2	RefSeq	NP_001342126.2	4	MANE Select
ENST00000344519.10	Ensembl	ENSP00000461425.1	4	MANE Select
ENST00000360204.5	Ensembl	ENSP00000459415.1	2	Standard
ENST00000594534.5	Ensembl	ENSP00000469543.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000344519
Coding exons: 4
Length: 32813
Individuals with no LoFs: 123826
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 123828
p: 0.00000808

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-2.18	368	268	1.37	0.0000128	3752
Missense (PolyPhen)		112	105.77	1.0589		1489
Synonymous	-3.56	133	90.0	1.48	0.00000405	977
Loss of Function	0.895	2	3.91	0.512	1.65e-7	57

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000057	0.000055	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000089	0.0000089	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in transcriptional regulation. {ECO:0000250}.;

Gene Damage Prediction

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