ZNF578

zinc finger protein 578, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:52453553-52516882

Links

ENSG00000258405 ∙ NCBI:147660 ∙ ∙ HGNC:26449 ∙ Uniprot:Q96N58 ∙ 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 ZNF578 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF578 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			33	1		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	2	0

Variants in ZNF578

This is a list of pathogenic ClinVar variants found in the ZNF578 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-52501853-A-G		not specified	Uncertain significance (Jun 06, 2023)
19-52501862-C-T		not specified	Uncertain significance (Oct 22, 2021)
19-52504676-G-A		not specified	Uncertain significance (Oct 08, 2024)
19-52504690-C-G		not specified	Uncertain significance (Aug 20, 2024)
19-52504722-C-T		not specified	Uncertain significance (Oct 04, 2022)
19-52510586-C-T		not specified	Likely benign (Aug 30, 2022)
19-52510677-G-T		not specified	Uncertain significance (Apr 19, 2024)
19-52510706-G-C		not specified	Uncertain significance (Jun 09, 2022)
19-52510761-C-G		not specified	Uncertain significance (Feb 02, 2022)
19-52510768-G-C		not specified	Uncertain significance (Sep 14, 2023)
19-52510797-C-A		not specified	Uncertain significance (Aug 14, 2024)
19-52510818-A-G		not specified	Uncertain significance (Feb 28, 2023)
19-52510832-C-G		not specified	Uncertain significance (Aug 27, 2024)
19-52510857-G-C		not specified	Uncertain significance (Aug 15, 2023)
19-52510877-G-C		not specified	Uncertain significance (Jun 07, 2023)
19-52510971-C-G		not specified	Uncertain significance (Dec 22, 2023)
19-52510974-G-A		not specified	Uncertain significance (Dec 14, 2023)
19-52511013-A-T		not specified	Uncertain significance (Oct 05, 2022)
19-52511052-T-C		not specified	Uncertain significance (Nov 15, 2024)
19-52511130-A-G		not specified	Uncertain significance (Aug 22, 2023)
19-52511157-A-G		not specified	Uncertain significance (May 05, 2023)
19-52511196-G-A		not specified	Uncertain significance (May 08, 2024)
19-52511241-A-T		not specified	Uncertain significance (Aug 14, 2024)
19-52511287-G-T			Likely benign (Apr 01, 2024)
19-52511330-T-C		not specified	Uncertain significance (Apr 25, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF578	protein_coding	protein_coding	ENST00000421239	3	58579

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00131	0.431	125605	0	79	125684	0.000314

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.796	347	308	1.13	0.0000158	3939
Missense in Polyphen		129	115.41	1.1178		1660
Synonymous	0.654	95	103	0.918	0.00000493	1008
Loss of Function	-0.152	4	3.69	1.09	1.55e-7	46

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000307	0.000305
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000519	0.000519
Middle Eastern	0.00	0.00
South Asian	0.000229	0.000229
Other	0.000653	0.000653

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.

Intolerance Scores

• loftool: 0.881
• rvis_EVS: 1.05
• rvis_percentile_EVS: 91.34

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

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, DNA-templated
• Cellular component: nucleus
• Molecular function: DNA binding;metal ion binding