ZNF562

zinc finger protein 562, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:9641807-9675100

Links

ENSG00000171466 ∙ NCBI:54811 ∙ ∙ HGNC:25950 ∙ Uniprot:Q6V9R5 ∙ 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 ZNF562 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF562 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			27	5		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	5	0

Variants in ZNF562

This is a list of pathogenic ClinVar variants found in the ZNF562 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-9653061-T-C		not specified	Uncertain significance (Oct 22, 2021)
19-9653073-G-A		not specified	Uncertain significance (Feb 08, 2025)
19-9653094-T-C		not specified	Uncertain significance (Jun 07, 2024)
19-9653130-G-C		not specified	Likely benign (May 04, 2023)
19-9653169-G-C		not specified	Uncertain significance (Nov 06, 2023)
19-9653188-C-T		not specified	Uncertain significance (Dec 16, 2022)
19-9653233-G-C		not specified	Uncertain significance (Sep 02, 2024)
19-9653274-G-A		not specified	Uncertain significance (Jul 09, 2021)
19-9653310-A-C		not specified	Uncertain significance (Aug 04, 2023)
19-9653325-G-C		not specified	Uncertain significance (Mar 19, 2024)
19-9653341-A-G		not specified	Uncertain significance (Nov 18, 2023)
19-9653365-C-G		not specified	Uncertain significance (Feb 06, 2023)
19-9653385-T-C		not specified	Uncertain significance (Jun 24, 2022)
19-9653400-G-A		not specified	Uncertain significance (Jan 17, 2023)
19-9653438-G-T		not specified	Likely benign (Sep 24, 2024)
19-9653460-T-C		not specified	Likely benign (Apr 12, 2024)
19-9653483-C-A		not specified	Uncertain significance (Jan 27, 2025)
19-9653576-G-T		not specified	Uncertain significance (Sep 17, 2021)
19-9653604-C-G		not specified	Uncertain significance (Jan 18, 2022)
19-9653673-G-T		not specified	Uncertain significance (Sep 29, 2023)
19-9653689-A-G		not specified	Uncertain significance (Jul 02, 2024)
19-9653704-A-G		not specified	Uncertain significance (Nov 05, 2021)
19-9653739-C-T		not specified	Uncertain significance (Jan 27, 2025)
19-9653743-T-G		not specified	Likely benign (Jun 13, 2023)
19-9653745-C-A		not specified	Likely benign (Jun 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF562	protein_coding	protein_coding	ENST00000448622	5	26447

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0569	0.873	125709	0	5	125714	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0954	214	218	0.982	0.0000101	2823
Missense in Polyphen		56	64.362	0.87007		849
Synonymous	-1.02	87	75.7	1.15	0.00000375	766
Loss of Function	1.52	3	7.48	0.401	3.16e-7	94

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)	0.0000177	0.0000176
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)

Intolerance Scores

• loftool: 0.823
• rvis_EVS: 0.57
• rvis_percentile_EVS: 82.08

Haploinsufficiency Scores

• pHI: 0.161
• hipred: N
• hipred_score: 0.174
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.175

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