ZNF560

zinc finger protein 560, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:9466354-9498616

Links

ENSG00000198028 ∙ NCBI:147741 ∙ ∙ HGNC:26484 ∙ Uniprot:Q96MR9 ∙ 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 ZNF560 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF560 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			52	1		53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	2	0

Variants in ZNF560

This is a list of pathogenic ClinVar variants found in the ZNF560 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-9466599-C-T		not specified	Uncertain significance (Aug 13, 2021)
19-9466629-C-A		not specified	Uncertain significance (Sep 27, 2022)
19-9466659-A-C		not specified	Uncertain significance (Sep 01, 2021)
19-9466790-T-A		not specified	Uncertain significance (Apr 11, 2023)
19-9466831-G-C		not specified	Uncertain significance (Jan 12, 2024)
19-9466882-A-C		not specified	Uncertain significance (May 14, 2024)
19-9466915-G-A		not specified	Uncertain significance (Jul 12, 2022)
19-9466932-G-A		not specified	Uncertain significance (Sep 26, 2023)
19-9467016-A-T		not specified	Uncertain significance (Mar 05, 2024)
19-9467032-C-T		not specified	Uncertain significance (Jun 17, 2024)
19-9467036-A-C		not specified	Uncertain significance (Jun 10, 2024)
19-9467076-C-G		not specified	Uncertain significance (Aug 17, 2021)
19-9467080-T-C		not specified	Uncertain significance (Nov 07, 2022)
19-9467113-G-A		not specified	Uncertain significance (Aug 14, 2023)
19-9467197-G-A		not specified	Uncertain significance (Nov 30, 2022)
19-9467276-T-C		not specified	Likely benign (Oct 27, 2023)
19-9467340-C-T		not specified	Likely benign (Feb 28, 2024)
19-9467343-A-G		not specified	Uncertain significance (Aug 23, 2021)
19-9467348-A-C		not specified	Uncertain significance (Mar 06, 2023)
19-9467355-A-G		not specified	Uncertain significance (Nov 07, 2022)
19-9467385-C-A		not specified	Uncertain significance (Jun 28, 2023)
19-9467442-G-T		not specified	Uncertain significance (Sep 13, 2022)
19-9467472-T-C		not specified	Uncertain significance (Dec 13, 2022)
19-9467487-C-T		not specified	Uncertain significance (Jan 16, 2024)
19-9467511-C-G		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF560	protein_coding	protein_coding	ENST00000301480	8	32101

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000967	0.799	125736	0	4	125740	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.327	425	406	1.05	0.0000203	5219
Missense in Polyphen		69	76.822	0.89819		952
Synonymous	-0.402	148	142	1.04	0.00000678	1422
Loss of Function	1.27	10	15.4	0.651	6.53e-7	182

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.000107	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)

Intolerance Scores

• loftool: 0.937
• rvis_EVS: -0.46
• rvis_percentile_EVS: 23.63

Haploinsufficiency Scores

• pHI: 0.153
• hipred: N
• hipred_score: 0.112
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.542

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp560

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