ZNF579

protein-coding

zinc finger protein 579, the group of Zinc fingers C2H2-type

Gene summary

Enables DNA-binding transcription factor activity, RNA polymerase II-specific and transcription cis-regulatory region binding activity. Involved in regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_152600.3

Inheritance

—

ClinVar variants

U:81

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr19:55,576,774-55,580,848

External References & Databases

Ensembl (ENSG00000218891)

Transcript & Mutation Effects

hg38 • Region Span ~4.1 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 ZNF579 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 79

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152600.3. 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			79 clinvar			79
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	81	0	0	81

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152600.3	RefSeq	NP_689813.2	1	MANE Select
ENST00000325421.7	Ensembl	ENSP00000320188.3	1	MANE Select
ENST00000592239.1	Ensembl	ENSP00000465146.1	1	Standard
ENST00000856087.1	Ensembl	ENSP00000526146.1	1	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
RNA binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000325421
Coding exons: 1
Length: 3313
Individuals with no LoFs: 115311
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 115312
p: 0.00000434

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.46	149	261	0.571	0.0000208	3448
Missense (PolyPhen)		34	87.695	0.38771		1220
Synonymous	2.40	92	126	0.728	0.0000108	1270
Loss of Function	2.70	1	10.4	0.0963	6.29e-7	141

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	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000098	0.0000098	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.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): H
Indispensability pred.: N
Indispensability score: 0.469

Gene Damage Prediction

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