ZNF586

zinc finger protein 586, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:57769655-57819939

Links

ENSG00000083828 ∙ NCBI:54807 ∙ ∙ HGNC:25949 ∙ Uniprot:Q9NXT0 ∙ 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 ZNF586 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF586 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			17	4		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	17	4	0

Variants in ZNF586

This is a list of pathogenic ClinVar variants found in the ZNF586 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-57769852-G-T		not specified	Uncertain significance (Sep 16, 2021)
19-57769853-C-T		not specified	Uncertain significance (Sep 16, 2021)
19-57776636-A-C		not specified	Uncertain significance (Mar 25, 2024)
19-57776659-A-G		not specified	Uncertain significance (Dec 07, 2021)
19-57778799-C-T		not specified	Uncertain significance (Jan 17, 2023)
19-57778805-T-C		not specified	Uncertain significance (May 14, 2024)
19-57778809-T-C		not specified	Likely benign (Jan 30, 2024)
19-57778933-C-T		not specified	Uncertain significance (Jul 20, 2021)
19-57778934-G-A		not specified	Likely benign (Jan 17, 2024)
19-57778978-T-C		not specified	Uncertain significance (Oct 12, 2021)
19-57779016-T-C		not specified	Likely benign (Dec 18, 2023)
19-57779087-A-T		not specified	Uncertain significance (Nov 01, 2022)
19-57779090-G-A		not specified	Likely benign (Nov 11, 2024)
19-57779096-C-T		not specified	Uncertain significance (Mar 08, 2024)
19-57779114-G-A		not specified	Likely benign (Feb 16, 2023)
19-57779128-A-G		not specified	Uncertain significance (Apr 26, 2023)
19-57779135-G-A		not specified	Uncertain significance (Nov 21, 2024)
19-57779164-C-G		not specified	Uncertain significance (Aug 27, 2024)
19-57779190-T-A		not specified	Likely benign (Aug 27, 2024)
19-57779243-C-T		not specified	Uncertain significance (Nov 30, 2022)
19-57779244-T-G		not specified	Likely benign (Nov 08, 2024)
19-57779283-G-A		not specified	Likely benign (Oct 24, 2024)
19-57779380-G-A		not specified	Uncertain significance (Oct 20, 2023)
19-57779405-G-A		not specified	Uncertain significance (Feb 15, 2023)
19-57779435-T-G		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF586	protein_coding	protein_coding	ENST00000396154	3	50285

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0365	0.648	125454	0	3	125457	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.201	211	219	0.962	0.0000114	2662
Missense in Polyphen		50	60.465	0.82693		799
Synonymous	-0.300	80	76.7	1.04	0.00000381	740
Loss of Function	0.384	2	2.68	0.747	1.14e-7	32

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)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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: 0.569
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.31

Haploinsufficiency Scores

• pHI: 0.0315
• hipred: N
• hipred_score: 0.112
• ghis: 0.484

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.128

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