ZNF564

zinc finger protein 564, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:12525373-12551542

Links

ENSG00000249709 ∙ NCBI:163050 ∙ ∙ HGNC:31106 ∙ Uniprot:Q8TBZ8 ∙ 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 ZNF564 gene.

• Deficiency of alpha-mannosidase (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF564 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			31	1		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	1					1
Total	1	0	31	1	0

Variants in ZNF564

This is a list of pathogenic ClinVar variants found in the ZNF564 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-12526468-G-A		not specified	Uncertain significance (Jan 17, 2024)
19-12526496-C-G		not specified	Uncertain significance (Oct 05, 2023)
19-12526519-T-C		not specified	Uncertain significance (Nov 21, 2022)
19-12526525-T-C		not specified	Uncertain significance (Aug 21, 2023)
19-12526552-G-C		not specified	Uncertain significance (Dec 06, 2022)
19-12526568-A-T		not specified	Uncertain significance (Sep 16, 2021)
19-12526597-G-A		not specified	Uncertain significance (Jan 10, 2023)
19-12526607-C-T		not specified	Uncertain significance (Sep 12, 2023)
19-12526630-C-G		not specified	Uncertain significance (Feb 11, 2022)
19-12526681-G-A		not specified	Uncertain significance (Jan 26, 2022)
19-12526874-C-T		not specified	Uncertain significance (Nov 22, 2021)
19-12526928-T-C		not specified	Uncertain significance (Dec 14, 2023)
19-12526966-C-T		not specified	Uncertain significance (Oct 02, 2023)
19-12526991-C-T		not specified	Uncertain significance (Oct 05, 2021)
19-12526997-C-T		not specified	Uncertain significance (Jan 24, 2024)
19-12527010-T-A		not specified	Uncertain significance (Jan 03, 2024)
19-12527122-C-A		not specified	Uncertain significance (Jun 22, 2021)
19-12527233-G-C		not specified	Uncertain significance (Feb 17, 2024)
19-12527404-A-C		not specified	Uncertain significance (Oct 26, 2022)
19-12527463-A-C		not specified	Uncertain significance (Sep 01, 2021)
19-12527503-C-T		not specified	Uncertain significance (Dec 28, 2022)
19-12527522-G-A		not specified	Uncertain significance (Apr 01, 2024)
19-12527524-C-G		not specified	Uncertain significance (Apr 25, 2022)
19-12527567-G-A		not specified	Uncertain significance (Jul 06, 2021)
19-12527603-A-T		not specified	Uncertain significance (Apr 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF564	protein_coding	protein_coding	ENST00000339282	4	26173

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.355	0.596	125570	0	5	125575	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	241	293	0.823	0.0000142	3693
Missense in Polyphen		58	92.189	0.62914		1165
Synonymous	-0.596	106	98.5	1.08	0.00000486	970
Loss of Function	1.55	1	4.57	0.219	1.93e-7	57

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)	0.0000450	0.0000440
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: 0.727
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.25

Haploinsufficiency Scores

• pHI: 0.188
• hipred: N
• hipred_score: 0.197
• ghis: 0.561

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.927

Gene Damage Prediction

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

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;transcription regulatory region DNA binding;metal ion binding