ZNF543

zinc finger protein 543, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:57320472-57330770

Links

ENSG00000178229 ∙ NCBI:125919 ∙ OMIM:616847 ∙ HGNC:25281 ∙ Uniprot:Q08ER8 ∙ 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 ZNF543 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF543 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			59	2		61
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	59	3	0

Variants in ZNF543

This is a list of pathogenic ClinVar variants found in the ZNF543 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-57323688-G-T		not specified	Uncertain significance (Apr 19, 2023)
19-57323748-G-T		not specified	Uncertain significance (Jan 30, 2024)
19-57323784-A-G		not specified	Uncertain significance (Apr 25, 2022)
19-57323803-C-T		not specified	Uncertain significance (Oct 05, 2023)
19-57326636-G-A		not specified	Uncertain significance (Mar 18, 2024)
19-57326690-G-A			Likely benign (Jun 18, 2018)
19-57327746-A-C		not specified	Uncertain significance (Nov 09, 2024)
19-57327781-C-G		not specified	Uncertain significance (Aug 02, 2021)
19-57327788-C-G		not specified	Uncertain significance (Jan 04, 2024)
19-57327796-G-C		not specified	Uncertain significance (Apr 14, 2022)
19-57327824-C-G		not specified	Uncertain significance (Feb 11, 2025)
19-57327892-G-T		not specified	Uncertain significance (Mar 12, 2024)
19-57327926-A-T		not specified	Uncertain significance (Nov 24, 2024)
19-57327928-G-T		not specified	Uncertain significance (Nov 24, 2024)
19-57327929-G-T		not specified	Uncertain significance (Nov 24, 2024)
19-57327952-T-C		not specified	Uncertain significance (Nov 26, 2024)
19-57327982-A-G		not specified	Uncertain significance (Feb 09, 2025)
19-57328012-C-T		not specified	Uncertain significance (Dec 16, 2024)
19-57328062-A-T		not specified	Uncertain significance (May 04, 2023)
19-57328142-A-G		not specified	Uncertain significance (Apr 08, 2024)
19-57328226-A-G		not specified	Uncertain significance (Feb 05, 2025)
19-57328258-C-T		not specified	Uncertain significance (Feb 10, 2022)
19-57328259-G-A		not specified	Uncertain significance (Dec 17, 2024)
19-57328286-G-A		not specified	Uncertain significance (May 25, 2022)
19-57328306-C-G		not specified	Uncertain significance (Dec 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF543	protein_coding	protein_coding	ENST00000321545	4	10268

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.52e-17	0.00141	125637	0	111	125748	0.000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.589	363	333	1.09	0.0000187	3968
Missense in Polyphen		146	115.92	1.2595		1480
Synonymous	-0.626	130	121	1.07	0.00000652	1097
Loss of Function	-0.798	23	19.2	1.20	9.70e-7	256

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00110	0.00109
Ashkenazi Jewish	0.00129	0.00129
East Asian	0.000326	0.000326
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000413	0.000413
Middle Eastern	0.000326	0.000326
South Asian	0.000653	0.000653
Other	0.000489	0.000489

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: 0.741
• rvis_EVS: 0.91
• rvis_percentile_EVS: 89.54

Haploinsufficiency Scores

• pHI: 0.0935
• hipred: N
• hipred_score: 0.112
• ghis: 0.463

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.377

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;protein binding;metal ion binding