ZNF558

zinc finger protein 558, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:8806170-8832314

Links

ENSG00000167785 ∙ NCBI:148156 ∙ ∙ HGNC:26422 ∙ Uniprot:Q96NG5 ∙ 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 ZNF558 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF558 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in ZNF558

This is a list of pathogenic ClinVar variants found in the ZNF558 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-8811304-T-C		not specified	Uncertain significance (Dec 05, 2022)
19-8811378-G-A		not specified	Uncertain significance (Mar 28, 2024)
19-8811460-C-T		not specified	Uncertain significance (Oct 14, 2023)
19-8811729-T-A		not specified	Uncertain significance (Jan 03, 2024)
19-8812050-C-T		not specified	Uncertain significance (Feb 15, 2023)
19-8812562-G-A		not specified	Uncertain significance (Apr 23, 2024)
19-8812596-C-T		not specified	Uncertain significance (Jul 14, 2023)
19-8812605-T-C		not specified	Uncertain significance (May 25, 2022)
19-8813131-A-C		not specified	Uncertain significance (Oct 29, 2021)
19-8813132-C-T		not specified	Uncertain significance (Aug 16, 2021)
19-8813150-C-T		not specified	Uncertain significance (Oct 05, 2023)
19-8813217-G-A		not specified	Uncertain significance (Apr 05, 2023)
19-8821192-G-C		not specified	Uncertain significance (Oct 26, 2022)
19-8821210-G-C		not specified	Uncertain significance (May 27, 2022)
19-8821235-T-G		not specified	Uncertain significance (Apr 15, 2024)
19-8822004-C-T		not specified	Likely benign (May 23, 2024)
19-8822005-G-A		not specified	Uncertain significance (May 23, 2023)
19-8822041-C-T		not specified	Uncertain significance (Dec 01, 2022)
19-8822044-C-G		not specified	Uncertain significance (Jan 23, 2024)
19-8822634-G-A		not specified	Uncertain significance (Jan 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF558	protein_coding	protein_coding	ENST00000601372	6	22625

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000889	0.783	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.869	181	217	0.834	0.0000111	2663
Missense in Polyphen		56	87.086	0.64304		1126
Synonymous	-1.38	99	83.0	1.19	0.00000474	721
Loss of Function	1.24	10	15.2	0.658	6.34e-7	217

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000540	0.0000527
Middle Eastern	0.000109	0.000109
South Asian	0.000204	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.0986

Intolerance Scores

• loftool: 0.602
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.54

Haploinsufficiency Scores

• pHI: 0.157
• hipred: N
• hipred_score: 0.131
• ghis: 0.530

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.217

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp558

Gene ontology

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