ZNF580

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

Basic information

Region (hg38): 19:55635016-55643470

Links

ENSG00000213015 ∙ NCBI:51157 ∙ OMIM:617888 ∙ HGNC:29473 ∙ Uniprot:Q9UK33 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZNF580 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF580 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			8		1	9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	1

Variants in ZNF580

This is a list of pathogenic ClinVar variants found in the ZNF580 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-55642584-G-C		not specified	Uncertain significance (Feb 10, 2022)
19-55642599-A-C		not specified	Uncertain significance (Jul 27, 2023)
19-55642615-C-G		not specified	Uncertain significance (Oct 08, 2024)
19-55642648-C-T		not specified	Uncertain significance (Apr 18, 2023)
19-55642692-C-T		not specified	Uncertain significance (Aug 06, 2021)
19-55642707-G-A		not specified	Uncertain significance (Nov 27, 2023)
19-55642752-C-A			Benign (Jul 13, 2018)
19-55642789-G-A		not specified	Uncertain significance (Aug 10, 2024)
19-55642801-C-A		not specified	Uncertain significance (Dec 03, 2024)
19-55642856-C-G		not specified	Uncertain significance (Jul 16, 2024)
19-55642888-A-G		not specified	Uncertain significance (Apr 22, 2022)
19-55642944-G-A		not specified	Uncertain significance (Apr 06, 2024)
19-55642963-G-A		not specified	Uncertain significance (Mar 28, 2023)
19-55642981-G-A		not specified	Uncertain significance (Aug 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF580	protein_coding	protein_coding	ENST00000543039	1	8454

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.534	0.412	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.09	39	63.4	0.615	0.00000305	1033
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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}.

Haploinsufficiency Scores

• pHI: 0.353
• hipred: N
• hipred_score: 0.368
• ghis: 0.471

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.534

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp580

Gene ontology

• Biological process: positive regulation of endothelial cell proliferation;positive regulation of leukocyte chemotaxis;regulation of transcription by RNA polymerase II;chemotaxis;inflammatory response;positive regulation of endothelial cell migration;positive regulation of gene expression;positive regulation of interleukin-8 production;cellular response to hydrogen peroxide
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding