ZNF578

protein-coding

zinc finger protein 578, 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 transcription by RNA polymerase II. Predicted to be located in cytoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001099694.2

Inheritance

—

ClinVar variants

U:106B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.09

Max pathogenic AF

—

Genomic locus

chr19:52,453,553-52,516,882

External References & Databases

Ensembl (ENSG00000258405)

Transcript & Mutation Effects

hg38 • Region Span ~63.3 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 ZNF578 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 107

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001099694.2. 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			1 clinvar	1 clinvar		2
missense			102 clinvar	6 clinvar		108
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	106	7	0	113

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_001099694.2	RefSeq	NP_001093164.1	3	MANE Select
ENST00000421239.7	Ensembl	ENSP00000459216.1	3	MANE Select
NM_001366182.2	RefSeq	NP_001353111.1	3	Standard
ENST00000601120.1	Ensembl	ENSP00000470790.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription, DNA-templated

Molecular Function

DNA binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000421239
Coding exons: 3
Length: 58579
Individuals with no LoFs: 125605
Homozygous LoFs: 0
Heterozygous LoFs: 79
Defined: 125684
p: 0.000314

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.796	347	308	1.13	0.0000158	3939
Missense (PolyPhen)		129	115.41	1.1178		1660
Synonymous	0.654	95	103	0.918	0.00000493	1008
Loss of Function	-0.152	4	3.69	1.09	1.55e-7	46

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00052	0.00052	rare
South Asian	0.00023	0.00023	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

LoFtool: 0.881
RVIS EVS: 1.05
RVIS percentile EVS: 91.34

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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