ZNF534

zinc finger protein 534, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:52429148-52452315

Previous symbols: [ "KRBO3" ]

Links

ENSG00000198633 ∙ NCBI:147658 ∙ ∙ HGNC:26337 ∙ Uniprot:Q76KX8 ∙ 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 ZNF534 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF534 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				2		2
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	5	0

Variants in ZNF534

This is a list of pathogenic ClinVar variants found in the ZNF534 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-52431487-C-A		Prostate cancer	Uncertain significance (-)
19-52433976-G-A		not specified	Uncertain significance (Aug 10, 2021)
19-52433995-A-C		not specified	Uncertain significance (Apr 06, 2023)
19-52434019-C-G		not specified	Uncertain significance (Jan 16, 2025)
19-52434049-T-C		not specified	Uncertain significance (Jan 09, 2025)
19-52434063-A-G		not specified	Uncertain significance (Aug 07, 2024)
19-52434081-G-C		not specified	Uncertain significance (Jun 10, 2022)
19-52434096-C-A		not specified	Uncertain significance (Feb 16, 2023)
19-52435139-G-T		not specified	Uncertain significance (Dec 03, 2024)
19-52435155-G-A		not specified	Uncertain significance (Jun 11, 2024)
19-52435177-A-G		not specified	Uncertain significance (Dec 06, 2021)
19-52437770-T-C		not specified	Likely benign (Jan 05, 2022)
19-52437802-G-T		not specified	Uncertain significance (Feb 01, 2023)
19-52437872-T-C		not specified	Uncertain significance (Aug 14, 2024)
19-52438007-G-A		not specified	Uncertain significance (Dec 12, 2024)
19-52438013-C-G		not specified	Uncertain significance (Aug 12, 2021)
19-52438025-A-C		not specified	Uncertain significance (Sep 17, 2021)
19-52438038-A-G		not specified	Uncertain significance (Mar 25, 2024)
19-52438070-C-T		not specified	Uncertain significance (Sep 11, 2024)
19-52438074-A-G		not specified	Uncertain significance (Jan 14, 2025)
19-52438092-A-G		not specified	Uncertain significance (Jan 31, 2025)
19-52438109-A-G		not specified	Uncertain significance (Apr 26, 2023)
19-52438121-G-A		not specified	Likely benign (Jan 01, 2025)
19-52438245-A-G		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
19-52438266-C-G		not specified	Uncertain significance (Jun 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF534	protein_coding	protein_coding	ENST00000332323	4	23129

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000129	0.120	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.350	334	352	0.948	0.0000179	4460
Missense in Polyphen		61	62.397	0.97762		828
Synonymous	0.393	118	124	0.955	0.00000591	1199
Loss of Function	-0.657	8	6.23	1.28	2.63e-7	76

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000182	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000153	0.000149
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000340	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation. {ECO:0000250}.

Intolerance Scores

• loftool: 0.697
• rvis_EVS: 2.98
• rvis_percentile_EVS: 99.2

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00444

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
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding