ZNF582

zinc finger protein 582, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:56375846-56393538

Links

ENSG00000018869 ∙ NCBI:147948 ∙ OMIM:615600 ∙ HGNC:26421 ∙ Uniprot:Q96NG8 ∙ 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 ZNF582 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF582 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				2	2	4
missense			19	1	1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	3	3

Variants in ZNF582

This is a list of pathogenic ClinVar variants found in the ZNF582 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-56383884-A-G		ZNF582-related disorder	Benign (Oct 28, 2019)
19-56383933-A-C		not specified	Uncertain significance (Jun 28, 2022)
19-56383939-G-A		not specified	Uncertain significance (Mar 16, 2022)
19-56383968-A-T		not specified	Uncertain significance (Aug 10, 2023)
19-56383975-A-G		not specified	Uncertain significance (Apr 20, 2023)
19-56383978-T-C		not specified	Uncertain significance (Apr 18, 2024)
19-56384018-C-T		not specified	Uncertain significance (Jan 17, 2024)
19-56384038-A-G		not specified	Uncertain significance (Feb 28, 2023)
19-56384081-T-C		not specified	Uncertain significance (Apr 01, 2024)
19-56384090-C-T		not specified	Uncertain significance (Apr 25, 2022)
19-56384127-C-T		ZNF582-related disorder	Benign (Oct 21, 2019)
19-56384149-T-C		not specified	Uncertain significance (Aug 19, 2021)
19-56384165-T-C		not specified	Uncertain significance (Jan 17, 2023)
19-56384210-C-T		not specified	Uncertain significance (May 09, 2023)
19-56384222-C-G		not specified	Uncertain significance (Jun 16, 2024)
19-56384238-T-C		ZNF582-related disorder	Likely benign (Jun 12, 2019)
19-56384368-T-C		not specified	Uncertain significance (Dec 13, 2023)
19-56384383-C-T			Uncertain significance (Dec 01, 2013)
19-56384519-C-G		not specified	Uncertain significance (May 30, 2024)
19-56384679-C-A		not specified	Uncertain significance (Jun 21, 2023)
19-56384685-T-A		not specified	Uncertain significance (Jul 20, 2022)
19-56384701-C-T		not specified	Uncertain significance (Dec 15, 2023)
19-56384707-T-C		not specified	Likely benign (Mar 25, 2024)
19-56384814-A-G			Likely benign (Oct 01, 2022)
19-56384842-A-C		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF582	protein_coding	protein_coding	ENST00000301310	4	17502

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000525	0.471	125695	0	53	125748	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.408	253	272	0.930	0.0000129	3451
Missense in Polyphen		92	110.03	0.83616		1375
Synonymous	0.139	94	95.7	0.982	0.00000477	878
Loss of Function	0.167	5	5.42	0.922	2.30e-7	61

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000466	0.000466
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000281	0.000281
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.833
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.73

Haploinsufficiency Scores

• pHI: 0.145
• hipred: N
• hipred_score: 0.132
• ghis: 0.556

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.558

Gene Damage Prediction

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