ZNF559

zinc finger protein 559, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:9323772-9351162

Links

ENSG00000188321 ∙ NCBI:84527 ∙ ∙ HGNC:28197 ∙ Uniprot:Q9BR84 ∙ 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 ZNF559 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF559 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			41	2	1	44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			7	1		8
Total	0	0	48	3	1

Variants in ZNF559

This is a list of pathogenic ClinVar variants found in the ZNF559 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-9324185-A-C		not specified	Uncertain significance (Mar 24, 2023)
19-9324195-C-T		not specified	Uncertain significance (Jan 04, 2022)
19-9324209-C-G		not specified	Uncertain significance (Mar 24, 2023)
19-9324215-C-G		not specified	Uncertain significance (Apr 20, 2024)
19-9324216-G-T		not specified	Likely benign (Feb 23, 2023)
19-9324222-G-T		not specified	Uncertain significance (Sep 16, 2021)
19-9324706-C-T		not specified	Uncertain significance (Dec 15, 2023)
19-9324741-C-T		not specified	Uncertain significance (Dec 28, 2023)
19-9324768-C-A		not specified	Uncertain significance (Oct 26, 2022)
19-9338566-T-G			Benign (Aug 08, 2017)
19-9338574-T-C		not specified	Uncertain significance (Jun 29, 2023)
19-9339221-T-C		not specified	Uncertain significance (Dec 28, 2023)
19-9339224-A-G		not specified	Uncertain significance (Mar 28, 2023)
19-9339299-A-G		not specified	Uncertain significance (Nov 08, 2022)
19-9341107-G-A		not specified	Uncertain significance (Aug 15, 2023)
19-9341161-A-G		not specified	Uncertain significance (May 24, 2024)
19-9341737-T-A		not specified	Uncertain significance (Mar 25, 2024)
19-9341845-T-A		not specified	Uncertain significance (Sep 16, 2021)
19-9341884-G-A		not specified	Likely benign (Mar 08, 2024)
19-9341929-C-G		not specified	Uncertain significance (Feb 05, 2024)
19-9341966-A-C		not specified	Uncertain significance (Jul 20, 2021)
19-9341977-A-G		not specified	Uncertain significance (Dec 30, 2023)
19-9342035-C-T		not specified	Uncertain significance (Dec 27, 2023)
19-9342044-C-T		not specified	Uncertain significance (Dec 17, 2021)
19-9342071-A-T		not specified	Uncertain significance (Dec 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF559	protein_coding	protein_coding	ENST00000393883	4	27391

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000142	0.241	125728	0	3	125731	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.05	325	276	1.18	0.0000127	3571
Missense in Polyphen		69	61.967	1.1135		799
Synonymous	-0.847	107	96.4	1.11	0.00000460	959
Loss of Function	-0.232	7	6.37	1.10	2.72e-7	71

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000594	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.0000594	0.0000544
South Asian	0.00	0.00
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: 0.0946

Intolerance Scores

• loftool: 0.955
• rvis_EVS: 0.73
• rvis_percentile_EVS: 86.3

Haploinsufficiency Scores

• pHI: 0.166
• hipred: N
• hipred_score: 0.112
• ghis: 0.544

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.859

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