ZNF652

zinc finger protein 652, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 17:49289205-49362473

Links

ENSG00000198740 ∙ NCBI:22834 ∙ OMIM:613907 ∙ HGNC:29147 ∙ Uniprot:Q9Y2D9 ∙ 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 ZNF652 gene.

• Inborn genetic diseases (22 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF652 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			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	0

Variants in ZNF652

This is a list of pathogenic ClinVar variants found in the ZNF652 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-49298522-G-A		not specified	Uncertain significance (Dec 19, 2022)
17-49298715-G-A		not specified	Uncertain significance (Sep 17, 2021)
17-49298754-C-A		not specified	Uncertain significance (May 11, 2022)
17-49312700-A-C		not specified	Uncertain significance (Dec 20, 2022)
17-49312701-C-T		not specified	Uncertain significance (Sep 21, 2021)
17-49312785-C-T		not specified	Uncertain significance (Apr 11, 2023)
17-49316833-T-C		not specified	Uncertain significance (Sep 20, 2023)
17-49316843-A-G			Uncertain significance (Nov 01, 2022)
17-49316956-C-T		not specified	Uncertain significance (Jan 17, 2023)
17-49316984-C-T		not specified	Uncertain significance (Dec 07, 2023)
17-49317053-G-A		not specified	Uncertain significance (Jun 23, 2023)
17-49317154-C-T		not specified	Uncertain significance (May 31, 2023)
17-49317167-C-T		not specified	Uncertain significance (Nov 22, 2021)
17-49317182-C-T		not specified	Uncertain significance (Aug 05, 2023)
17-49317290-C-G		not specified	Uncertain significance (May 11, 2022)
17-49317310-G-A		not specified	Uncertain significance (Apr 07, 2022)
17-49317445-T-G		not specified	Uncertain significance (Sep 26, 2023)
17-49317458-C-T		not specified	Uncertain significance (Mar 17, 2023)
17-49317503-T-C		not specified	Uncertain significance (Oct 05, 2023)
17-49317508-T-C		not specified	Uncertain significance (Jul 19, 2023)
17-49317538-A-G		not specified	Uncertain significance (May 27, 2022)
17-49317568-C-G		not specified	Uncertain significance (Jun 24, 2022)
17-49317580-T-C		not specified	Uncertain significance (Dec 05, 2022)
17-49317603-G-C		not specified	Uncertain significance (Mar 29, 2022)
17-49317640-C-T		not specified	Uncertain significance (Jul 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF652	protein_coding	protein_coding	ENST00000362063	5	73268

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.823	0.177	125737	0	7	125744	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.35	229	353	0.649	0.0000194	4065
Missense in Polyphen		44	103.78	0.42399		1211
Synonymous	0.463	117	124	0.947	0.00000673	1111
Loss of Function	3.39	3	18.9	0.159	7.96e-7	274

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000581	0.0000581
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a transcriptional repressor. {ECO:0000269|PubMed:16966434}.

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.0254
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.26

Haploinsufficiency Scores

• pHI: 0.231
• hipred: Y
• hipred_score: 0.642
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.423

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp652

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;cellular response to DNA damage stimulus
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;metal ion binding