ZNF593

zinc finger protein 593, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 1:26169907-26170873

Links

ENSG00000142684 ∙ NCBI:51042 ∙ OMIM:616698 ∙ HGNC:30943 ∙ Uniprot:O00488 ∙ 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 ZNF593 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF593 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in ZNF593

This is a list of pathogenic ClinVar variants found in the ZNF593 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-26170029-G-T		not specified	Uncertain significance (Jan 17, 2024)
1-26170077-C-T		not specified	Uncertain significance (Feb 17, 2022)
1-26170093-C-T		not specified	Uncertain significance (Mar 11, 2024)
1-26170115-G-C		not specified	Uncertain significance (May 30, 2023)
1-26170125-A-C		not specified	Uncertain significance (Jan 23, 2023)
1-26170131-G-A		not specified	Uncertain significance (Jul 26, 2021)
1-26170132-A-C		not specified	Uncertain significance (Jun 26, 2023)
1-26170431-G-A		not specified	Uncertain significance (Jun 06, 2023)
1-26170467-G-T		not specified	Uncertain significance (Dec 02, 2022)
1-26170601-A-G		not specified	Uncertain significance (Sep 26, 2022)
1-26170678-G-A		not specified	Uncertain significance (Jan 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF593	protein_coding	protein_coding	ENST00000374266	3	2190

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000665	0.520	125726	0	7	125733	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.755	62	81.1	0.764	0.00000428	830
Missense in Polyphen		18	17.58	1.0239		200
Synonymous	1.50	25	36.5	0.684	0.00000202	284
Loss of Function	0.303	5	5.79	0.864	3.20e-7	53

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negatively modulates the DNA binding activity of Oct-2 and therefore its transcriptional regulatory activity. Could act either by binding to DNA octamer or by interacting with Oct-2. May also be a modulator of other octamer-binding proteins.

Haploinsufficiency Scores

• pHI: 0.260
• hipred: Y
• hipred_score: 0.672

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.776

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp593

Gene ontology

• Biological process: ribosomal large subunit export from nucleus;positive regulation of transcription by RNA polymerase II;negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding
• Cellular component: nucleus;nucleolus;preribosome, large subunit precursor
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;zinc ion binding;ribosomal large subunit binding