ZNF652

protein-coding

zinc finger protein 652, the group of Zinc fingers C2H2-type

Gene summary

Enables DNA-binding transcription repressor activity, RNA polymerase II-specific. Involved in negative regulation of transcription by RNA polymerase II. Is active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001145365.3

Inheritance

—

ClinVar variants

U:80B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr17:49,289,206-49,362,473

External References & Databases

Ensembl (ENSG00000198740)

Transcript & Mutation Effects

hg38 • Region Span ~73.3 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 ZNF652 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 75

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001145365.3. 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			2 clinvar			2
missense			78 clinvar	1 clinvar		79
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	80	1	0	81

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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_001145365.3	RefSeq	NP_001138837.1	5	MANE Select
ENST00000430262.3	Ensembl	ENSP00000416305.2	5	MANE Select
NM_014897.2	RefSeq	NP_055712.1	5	Standard
ENST00000362063.6	Ensembl	ENSP00000354686.2	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
cellular response to DNA damage stimulus

Molecular Function

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

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000362063
Coding exons: 5
Length: 73268
Individuals with no LoFs: 125737
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125744
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.35	229	353	0.649	0.0000194	4065
Missense (PolyPhen)		44	103.78	0.42399		1211
Synonymous	0.463	117	124	0.947	0.00000673	1111
Loss of Function	3.39	3	18.9	0.159	7.96e-7	274

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Functions as a transcriptional repressor. {ECO:0000269|PubMed:16966434}.;

Recessive Scores

pRec: 0.112

Intolerance Scores

LoFtool: 0.0254
RVIS EVS: -0.11
RVIS percentile EVS: 45.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.423

Gene Damage Prediction

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