ZNF584

zinc finger protein 584, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:58401504-58431736

Links

ENSG00000171574 ∙ NCBI:201514 ∙ ∙ HGNC:27318 ∙ Uniprot:Q8IVC4 ∙ 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 ZNF584 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF584 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			28	2		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	2	0

Variants in ZNF584

This is a list of pathogenic ClinVar variants found in the ZNF584 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-58409160-G-A		not specified	Uncertain significance (Dec 02, 2021)
19-58409942-C-T		not specified	Likely benign (May 26, 2024)
19-58409965-G-C		not specified	Uncertain significance (Jul 06, 2021)
19-58409974-A-T		not specified	Uncertain significance (Feb 22, 2023)
19-58409990-C-T		not specified	Uncertain significance (Oct 11, 2024)
19-58415529-G-C		not specified	Uncertain significance (Dec 15, 2023)
19-58415573-A-T		not specified	Uncertain significance (Sep 26, 2024)
19-58415578-C-T		not specified	Likely benign (Jan 20, 2025)
19-58415595-G-A		not specified	Uncertain significance (Jan 22, 2025)
19-58415598-G-A		not specified	Uncertain significance (Dec 08, 2023)
19-58416852-C-T		not specified	Uncertain significance (Apr 01, 2024)
19-58416864-T-A		not specified	Uncertain significance (Mar 07, 2025)
19-58416891-C-T		not specified	Uncertain significance (Jan 07, 2025)
19-58416897-G-A		not specified	Uncertain significance (Feb 27, 2025)
19-58416904-A-C		not specified	Uncertain significance (Nov 01, 2022)
19-58416913-G-A		not specified	Uncertain significance (Oct 06, 2021)
19-58416916-A-G		not specified	Uncertain significance (Aug 28, 2023)
19-58416951-A-G		not specified	Uncertain significance (May 20, 2024)
19-58417035-G-A		not specified	Uncertain significance (Feb 07, 2025)
19-58417041-C-T		not specified	Uncertain significance (Feb 28, 2025)
19-58417096-G-A		not specified	Uncertain significance (Sep 13, 2023)
19-58417120-A-T		not specified	Likely benign (Nov 29, 2023)
19-58417158-C-T		not specified	Uncertain significance (Apr 07, 2022)
19-58417195-C-T		not specified	Uncertain significance (Apr 20, 2024)
19-58417233-A-G		not specified	Uncertain significance (Jan 24, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF584	protein_coding	protein_coding	ENST00000306910	4	16824

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000105	0.826	125658	0	90	125748	0.000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.717	204	235	0.868	0.0000124	2782
Missense in Polyphen		74	86.987	0.85071		1013
Synonymous	-0.665	97	89.0	1.09	0.00000472	784
Loss of Function	1.25	8	12.8	0.623	6.25e-7	169

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000658	0.000658
Ashkenazi Jewish	0.00	0.00
East Asian	0.000435	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000519	0.000519
Middle Eastern	0.000435	0.000435
South Asian	0.000131	0.000131
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Intolerance Scores

• loftool: 0.802
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.71

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding