ZNF568

zinc finger protein 568, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:36916315-37005037

Links

ENSG00000198453 ∙ NCBI:374900 ∙ OMIM:617566 ∙ HGNC:25392 ∙ Uniprot:Q3ZCX4 ∙ 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 ZNF568 gene.

• Inborn genetic diseases (28 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF568 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				1	1	2
missense			28			28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	1	1

Variants in ZNF568

This is a list of pathogenic ClinVar variants found in the ZNF568 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-36922802-G-T		not specified	Uncertain significance (Oct 26, 2022)
19-36922829-A-G		not specified	Uncertain significance (Jan 10, 2022)
19-36922832-T-A		not specified	Uncertain significance (Dec 20, 2023)
19-36925253-C-A		not specified	Uncertain significance (Aug 17, 2021)
19-36936786-A-G		not specified	Uncertain significance (Mar 06, 2023)
19-36937167-G-T		not specified	Uncertain significance (Jun 29, 2023)
19-36949575-C-G		not specified	Uncertain significance (Mar 06, 2023)
19-36949771-G-T		not specified	Uncertain significance (Jan 16, 2024)
19-36949775-G-C		not specified	Uncertain significance (Nov 28, 2023)
19-36949776-G-C		not specified	Uncertain significance (Sep 26, 2022)
19-36949805-G-A		not specified	Uncertain significance (Jul 25, 2023)
19-36949837-A-G			Benign (Jan 08, 2018)
19-36949955-C-T		not specified	Uncertain significance (Aug 21, 2023)
19-36949986-A-G		not specified	Uncertain significance (Jul 13, 2021)
19-36950118-T-C		not specified	Uncertain significance (Nov 29, 2023)
19-36950130-G-A		not specified	Uncertain significance (Oct 26, 2022)
19-36950252-T-G		not specified	Uncertain significance (Oct 04, 2022)
19-36950255-G-T		not specified	Uncertain significance (Dec 04, 2021)
19-36950350-C-A		not specified	Uncertain significance (Jan 02, 2024)
19-36950413-T-G		not specified	Uncertain significance (Jul 09, 2021)
19-36950456-G-A		not specified	Uncertain significance (Aug 02, 2021)
19-36950570-C-A		not specified	Uncertain significance (Mar 06, 2023)
19-36950643-C-T		not specified	Uncertain significance (Dec 02, 2022)
19-36950669-G-A		not specified	Uncertain significance (Mar 29, 2023)
19-36950685-T-G		not specified	Uncertain significance (Mar 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF568	protein_coding	protein_coding	ENST00000333987	5	82372

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.28e-9	0.883	125506	0	218	125724	0.000867

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	262	338	0.775	0.0000159	4328
Missense in Polyphen		126	167.3	0.75312		2132
Synonymous	1.65	90	112	0.802	0.00000537	1087
Loss of Function	1.76	18	28.1	0.642	0.00000170	351

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00202	0.00201
Ashkenazi Jewish	0.00	0.00
East Asian	0.00131	0.00131
Finnish	0.00217	0.00217
European (Non-Finnish)	0.000505	0.000501
Middle Eastern	0.00131	0.00131
South Asian	0.000720	0.000719
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has transcriptional repression activity, partially through the recruitment of the corepressor TRIM28 but has also repression activity independently of this interaction. Essential during embryonic development, where it acts as direct repressor of a placental-specific transcript of IGF2 in early development and regulates convergent extension movements required for axis elongation and tissue morphogenesis in all germ layers. Also important for normal morphogenesis of extraembryonic tissues including the yolk sac, extraembryonic mesoderm and placenta. May enhance proliferation or maintenance of neural stem cells. {ECO:0000250|UniProtKB:E9PYI1}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.112
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.160

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;in utero embryonic development;negative regulation of transcription, DNA-templated;embryonic placenta morphogenesis
• Cellular component: nucleus
• Molecular function: transcription regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;metal ion binding