ZNF561

zinc finger protein 561, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:9604680-9621236

Links

ENSG00000171469 ∙ NCBI:93134 ∙ ∙ HGNC:28684 ∙ Uniprot:Q8N587 ∙ 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 ZNF561 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF561 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			42	3		45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	3	0

Variants in ZNF561

This is a list of pathogenic ClinVar variants found in the ZNF561 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-9610228-T-C		not specified	Uncertain significance (Feb 16, 2023)
19-9610297-C-T		not specified	Uncertain significance (Jan 04, 2024)
19-9610324-T-C		not specified	Uncertain significance (Nov 27, 2023)
19-9610357-C-T		not specified	Uncertain significance (Jan 17, 2023)
19-9610358-G-A		not specified	Uncertain significance (Aug 13, 2021)
19-9610381-C-T		not specified	Uncertain significance (Feb 16, 2023)
19-9610386-T-C		not specified	Uncertain significance (Mar 01, 2023)
19-9610438-C-T		not specified	Uncertain significance (Mar 02, 2023)
19-9610529-T-C		not specified	Uncertain significance (Mar 20, 2024)
19-9610531-G-A		not specified	Uncertain significance (Apr 07, 2023)
19-9610535-T-C		not specified	Uncertain significance (May 02, 2024)
19-9610568-A-T		not specified	Uncertain significance (Dec 05, 2022)
19-9610667-T-C		not specified	Uncertain significance (Mar 29, 2023)
19-9610675-C-T		not specified	Uncertain significance (Feb 23, 2023)
19-9610696-G-C		not specified	Uncertain significance (Sep 07, 2022)
19-9610705-G-T		not specified	Uncertain significance (Jul 12, 2022)
19-9610789-C-T		not specified	Uncertain significance (Mar 02, 2023)
19-9610819-A-T		not specified	Uncertain significance (Aug 22, 2023)
19-9610832-C-T		not specified	Uncertain significance (Dec 12, 2023)
19-9610835-T-C		not specified	Uncertain significance (Mar 28, 2024)
19-9610846-A-G		not specified	Uncertain significance (Oct 25, 2022)
19-9610849-G-T		not specified	Likely benign (Oct 25, 2022)
19-9610879-G-A		not specified	Uncertain significance (Dec 19, 2023)
19-9610904-T-C		not specified	Uncertain significance (Feb 23, 2023)
19-9610946-G-A		not specified	Uncertain significance (May 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF561	protein_coding	protein_coding	ENST00000302851	5	16720

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000301	0.352	125289	0	2	125291	0.00000798

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.247	269	258	1.04	0.0000126	3205
Missense in Polyphen		88	95.74	0.91916		1382
Synonymous	-1.43	104	87.0	1.20	0.00000410	896
Loss of Function	0.126	7	7.37	0.950	3.11e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000655	0.0000654
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: 0.698
• rvis_EVS: -0.96
• rvis_percentile_EVS: 9.09

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.174
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0473

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;DNA-binding transcription factor activity;metal ion binding