ZNF563

zinc finger protein 563, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:12317477-12333720

Links

ENSG00000188868 ∙ NCBI:147837 ∙ ∙ HGNC:30498 ∙ Uniprot:Q8TA94 ∙ 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 ZNF563 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF563 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			49	3		52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	49	3	0

Variants in ZNF563

This is a list of pathogenic ClinVar variants found in the ZNF563 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-12318611-A-G		not specified	Uncertain significance (May 07, 2024)
19-12318643-G-A		not specified	Uncertain significance (Nov 15, 2024)
19-12318644-G-A		not specified	Uncertain significance (May 30, 2024)
19-12318715-C-G		not specified	Uncertain significance (Jan 26, 2022)
19-12318734-A-G		not specified	Uncertain significance (Feb 11, 2022)
19-12318749-A-G		not specified	Uncertain significance (Jul 09, 2024)
19-12318824-C-G		not specified	Uncertain significance (Feb 12, 2024)
19-12318967-C-T		not specified	Uncertain significance (Jul 14, 2021)
19-12318983-G-A		not specified	Uncertain significance (Nov 17, 2022)
19-12319001-A-G		not specified	Uncertain significance (Aug 20, 2024)
19-12319021-C-T		not specified	Uncertain significance (Oct 04, 2024)
19-12319066-T-C		not specified	Uncertain significance (May 24, 2024)
19-12319069-T-A		not specified	Uncertain significance (Dec 14, 2023)
19-12319135-C-T		not specified	Uncertain significance (May 23, 2023)
19-12319139-G-A		not specified	Uncertain significance (Dec 17, 2023)
19-12319220-T-C		not specified	Uncertain significance (Jan 29, 2024)
19-12319270-G-A		not specified	Uncertain significance (Nov 25, 2024)
19-12319272-T-G		not specified	Uncertain significance (Dec 03, 2024)
19-12319303-C-A		not specified	Likely benign (Apr 01, 2024)
19-12319306-T-C		not specified	Uncertain significance (Mar 24, 2023)
19-12319366-G-C		not specified	Uncertain significance (Feb 10, 2022)
19-12319381-T-G		not specified	Uncertain significance (Sep 20, 2024)
19-12319388-G-A		not specified	Uncertain significance (Jun 01, 2023)
19-12319409-A-G		not specified	Uncertain significance (Feb 15, 2023)
19-12319429-C-A		not specified	Uncertain significance (Jul 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF563	protein_coding	protein_coding	ENST00000293725	4	16244

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.764	0.228	125489	0	20	125509	0.0000797

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.292	243	256	0.949	0.0000143	3195
Missense in Polyphen		93	92.305	1.0075		1275
Synonymous	0.219	81	83.5	0.970	0.00000472	808
Loss of Function	2.03	0	4.79	0.00	2.02e-7	59

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000948	0.0000924
European (Non-Finnish)	0.000109	0.000106
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000328
Other	0.000165	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: 0.729
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.36

Haploinsufficiency Scores

• pHI: 0.200
• hipred: N
• hipred_score: 0.112
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.219

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp563

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