ZNF557

zinc finger protein 557, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:7069703-7087968

Links

ENSG00000130544 ∙ NCBI:79230 ∙ ∙ HGNC:28632 ∙ Uniprot:Q8N988 ∙ 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 ZNF557 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF557 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				4		4
missense			22	5		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	22	9	0

Variants in ZNF557

This is a list of pathogenic ClinVar variants found in the ZNF557 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-7075096-C-G		not specified	Uncertain significance (Aug 14, 2023)
19-7075651-C-G			Likely benign (Nov 01, 2022)
19-7075672-C-T		not specified	Uncertain significance (Oct 05, 2022)
19-7075685-G-A		not specified	Likely benign (Nov 13, 2024)
19-7076408-G-T		not specified	Uncertain significance (Jul 17, 2024)
19-7076429-T-C		not specified	Uncertain significance (Jul 19, 2023)
19-7076472-T-C		not specified	Uncertain significance (Mar 11, 2022)
19-7076487-G-T		not specified	Likely benign (Nov 03, 2023)
19-7081410-A-G		not specified	Uncertain significance (Sep 14, 2021)
19-7081437-C-A		not specified	Uncertain significance (Jan 23, 2024)
19-7081996-G-A		not specified	Uncertain significance (Feb 12, 2024)
19-7082045-T-G		not specified	Uncertain significance (Oct 20, 2023)
19-7082891-T-G		not specified	Uncertain significance (Mar 21, 2023)
19-7082907-C-T			Likely benign (Jun 01, 2022)
19-7082919-G-T		not specified	Uncertain significance (Aug 23, 2021)
19-7082945-C-A		not specified	Uncertain significance (Mar 19, 2024)
19-7082954-C-G		not specified	Uncertain significance (Oct 29, 2021)
19-7083074-A-G		not specified	Uncertain significance (Dec 07, 2021)
19-7083082-A-G		not specified	Uncertain significance (Dec 09, 2023)
19-7083083-A-T		not specified	Uncertain significance (Jun 01, 2023)
19-7083159-C-T			Likely benign (Nov 01, 2022)
19-7083160-G-A		not specified	Likely benign (Dec 14, 2023)
19-7083215-T-C		not specified	Uncertain significance (Jan 03, 2024)
19-7083300-G-T		not specified	Uncertain significance (Jun 21, 2022)
19-7083307-C-A		not specified	Uncertain significance (Mar 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF557	protein_coding	protein_coding	ENST00000414706	6	18525

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0280	0.927	125732	0	14	125746	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.610	211	237	0.889	0.0000124	2847
Missense in Polyphen		43	47.943	0.8969		495
Synonymous	-0.724	104	95.0	1.09	0.00000566	795
Loss of Function	1.72	4	9.83	0.407	5.01e-7	107

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000214
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000619	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000981	0.0000980
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: 0.0639

Intolerance Scores

• loftool: 0.951
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.36

Haploinsufficiency Scores

• pHI: 0.0664
• hipred: N
• hipred_score: 0.112
• ghis: 0.489

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.189

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