ZNF566

zinc finger protein 566, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:36445118-36489902

Links

ENSG00000186017 ∙ NCBI:84924 ∙ ∙ HGNC:25919 ∙ Uniprot:Q969W8 ∙ 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 ZNF566 gene.

• Inborn genetic diseases (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF566 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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in ZNF566

This is a list of pathogenic ClinVar variants found in the ZNF566 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-36449185-G-A		not specified	Uncertain significance (Jan 16, 2024)
19-36449213-A-C		not specified	Uncertain significance (Jun 26, 2023)
19-36449399-C-G		not specified	Uncertain significance (Jan 22, 2024)
19-36449651-T-A		not specified	Uncertain significance (Apr 07, 2022)
19-36449713-T-C		not specified	Uncertain significance (Jun 18, 2021)
19-36449795-C-T		not specified	Uncertain significance (Nov 07, 2023)
19-36449815-T-C		not specified	Likely benign (Jan 24, 2023)
19-36449824-C-G		not specified	Uncertain significance (May 18, 2022)
19-36449863-C-T		not specified	Uncertain significance (May 26, 2023)
19-36449867-C-T		not specified	Uncertain significance (Nov 08, 2022)
19-36449903-G-A		not specified	Uncertain significance (Dec 15, 2023)
19-36472954-C-A		not specified	Uncertain significance (Dec 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF566	protein_coding	protein_coding	ENST00000454319	4	44784

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.415	0.585	125717	0	24	125741	0.0000954

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.738	186	217	0.859	0.0000102	2811
Missense in Polyphen		48	75.792	0.63332		975
Synonymous	0.594	67	73.5	0.912	0.00000351	697
Loss of Function	3.09	4	18.3	0.219	9.02e-7	247

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000163	0.000163
South Asian	0.00	0.00
Other	0.000163	0.000163

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: 0.929
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• pHI: 0.227
• hipred: N
• hipred_score: 0.383
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.779

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp566

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