ZNF580

protein-coding

zinc finger protein 580, the group of Zinc fingers C2H2-type

Gene summary

Enables sequence-specific double-stranded DNA binding activity. Involved in several processes, including cellular response to hydrogen peroxide; positive regulation of cell migration; and positive regulation of interleukin-8 production. Located in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_207115.2

Inheritance

—

ClinVar variants

U:25B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr19:55,635,016-55,643,470

External References & Databases

Ensembl (ENSG00000213015)

Transcript & Mutation Effects

hg38 • Region Span ~8.5 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 ZNF580 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 26

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_207115.2. 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						0
missense			25 clinvar	1 clinvar	1 clinvar	27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	25	1	1	27

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_207115.2	RefSeq	NP_996998.1	1	MANE Select
ENST00000325333.10	Ensembl	ENSP00000320050.4	1	MANE Select
NM_001163423.2	RefSeq	NP_001156895.1	1	Standard
NM_016202.2	RefSeq	NP_057286.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of endothelial cell proliferation
positive regulation of leukocyte chemotaxis
regulation of transcription by RNA polymerase II
chemotaxis
inflammatory response

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: ENST00000543039
Coding exons: 1
Length: 8454
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.09	39	63.4	0.615	0.00000305	1033
Missense (PolyPhen)		1	4.5632	0.21914		69
Synonymous	0.630	26	30.4	0.855	0.00000145	395
Loss of Function	1.39	0	2.24	0.00	9.94e-8	33

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	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in the regulation of endothelial cell proliferation and migration. Mediates H(2)O(2)-induced leukocyte chemotaxis by elevating interleukin-8 production and may play a role in inflammation. May be involved in transcriptional regulation. {ECO:0000269|PubMed:20382120, ECO:0000269|PubMed:21830064}.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.534

Gene Damage Prediction

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