ZNF594

zinc finger protein 594, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 17:5179535-5191868

Links

ENSG00000180626 ∙ NCBI:84622 ∙ ∙ HGNC:29392 ∙ Uniprot:Q96JF6 ∙ 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 ZNF594 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF594 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
missense			84	7		91
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	84	8	0

Variants in ZNF594

This is a list of pathogenic ClinVar variants found in the ZNF594 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-5181856-G-A		not specified	Uncertain significance (May 01, 2022)
17-5181904-T-C		not specified	Uncertain significance (Dec 11, 2024)
17-5181922-G-A		not specified	Uncertain significance (Dec 05, 2024)
17-5181925-T-C		not specified	Uncertain significance (Dec 11, 2024)
17-5181958-T-C			Likely benign (May 01, 2024)
17-5181979-C-T		not specified	Uncertain significance (Mar 25, 2024)
17-5182045-A-G		not specified	Uncertain significance (Oct 04, 2024)
17-5182075-T-C		not specified	Uncertain significance (Jan 01, 2025)
17-5182099-G-A		not specified	Uncertain significance (Dec 15, 2024)
17-5182112-T-C			Likely benign (Jun 01, 2022)
17-5182117-C-T		not specified	Uncertain significance (Nov 11, 2024)
17-5182123-C-G		not specified	Uncertain significance (Apr 12, 2023)
17-5182162-G-A		not specified	Uncertain significance (Nov 08, 2024)
17-5182183-G-A		not specified	Uncertain significance (Mar 07, 2025)
17-5182186-G-A		not specified	Uncertain significance (Feb 13, 2024)
17-5182186-G-C		not specified	Uncertain significance (Aug 26, 2024)
17-5182194-G-A		not specified	Uncertain significance (Nov 06, 2023)
17-5182203-C-T		not specified	Uncertain significance (Jan 16, 2024)
17-5182209-C-G		not specified	Uncertain significance (Jan 16, 2024)
17-5182213-A-G		not specified	Uncertain significance (May 24, 2024)
17-5182255-C-G		not specified	Uncertain significance (Feb 16, 2023)
17-5182260-T-G		not specified	Uncertain significance (Aug 01, 2024)
17-5182294-T-A		not specified	Uncertain significance (Jan 16, 2024)
17-5182324-T-C		not specified	Likely benign (Sep 25, 2023)
17-5182415-A-T		not specified	Uncertain significance (Jan 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF594	protein_coding	protein_coding	ENST00000399604	1	12348

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000926	0.354	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.50	549	407	1.35	0.0000197	5418
Missense in Polyphen		170	135.1	1.2584		1846
Synonymous	-1.72	159	134	1.19	0.00000607	1357
Loss of Function	-0.0185	6	5.95	1.01	2.46e-7	94

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)	0.00	0.00
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. {ECO:0000250}.

Intolerance Scores

• loftool: 0.874
• rvis_EVS: 1.18
• rvis_percentile_EVS: 92.83

Haploinsufficiency Scores

• pHI: 0.0568
• hipred: N
• hipred_score: 0.146
• ghis: 0.528

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.558

Gene Damage Prediction

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

Gene ontology

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