ZNF552

zinc finger protein 552, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:57803841-57814913

Links

ENSG00000178935 ∙ NCBI:79818 ∙ ∙ HGNC:26135 ∙ Uniprot:Q9H707 ∙ 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 ZNF552 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF552 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			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	0

Variants in ZNF552

This is a list of pathogenic ClinVar variants found in the ZNF552 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-57808095-C-G		not specified	Uncertain significance (Dec 01, 2022)
19-57808120-A-C		not specified	Uncertain significance (Dec 15, 2023)
19-57808245-C-A		not specified	Uncertain significance (Jul 19, 2023)
19-57808246-G-T		not specified	Uncertain significance (Jul 19, 2023)
19-57808247-G-C		not specified	Likely benign (Sep 16, 2021)
19-57808326-G-A		not specified	Uncertain significance (May 15, 2024)
19-57808465-G-A		not specified	Uncertain significance (Apr 19, 2023)
19-57808503-C-G		not specified	Uncertain significance (Jan 17, 2024)
19-57808571-C-G		not specified	Uncertain significance (Sep 01, 2021)
19-57808690-T-A		not specified	Uncertain significance (Jul 21, 2021)
19-57808695-G-C		not specified	Uncertain significance (Oct 04, 2022)
19-57808758-G-C		not specified	Uncertain significance (Aug 17, 2021)
19-57808844-C-G		not specified	Uncertain significance (Sep 29, 2023)
19-57808847-A-T		not specified	Uncertain significance (May 05, 2023)
19-57808978-A-C		not specified	Uncertain significance (Aug 02, 2021)
19-57808980-A-C		not specified	Uncertain significance (Aug 02, 2021)
19-57808982-C-G		not specified	Uncertain significance (Aug 02, 2021)
19-57809025-G-C		not specified	Uncertain significance (Mar 31, 2023)
19-57809061-T-C		not specified	Uncertain significance (Jan 26, 2022)
19-57813305-A-T		not specified	Uncertain significance (Dec 08, 2023)
19-57813336-G-A		not specified	Uncertain significance (Dec 01, 2022)
19-57813343-G-C		not specified	Uncertain significance (Jan 10, 2022)
19-57813366-G-C		not specified	Uncertain significance (Dec 01, 2022)
19-57813399-C-T		not specified	Uncertain significance (Dec 01, 2022)
19-57814715-A-C		not specified	Uncertain significance (Dec 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF552	protein_coding	protein_coding	ENST00000391701	3	11073

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000868	0.356	125718	1	25	125744	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.978	171	211	0.811	0.0000103	2707
Missense in Polyphen		60	66.838	0.89769		950
Synonymous	-1.16	94	80.8	1.16	0.00000437	729
Loss of Function	-0.473	4	3.10	1.29	1.32e-7	35

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00125	0.00120
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00125	0.00120
South Asian	0.00	0.00
Other	0.000163	0.000163

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: 0.722
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.73

Haploinsufficiency Scores

• pHI: 0.106
• hipred: N
• hipred_score: 0.187
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

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;negative regulation of transcription, DNA-templated
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding