ZNF653

zinc finger protein 653, the group of Zinc fingers C2H2-type|MicroRNA protein coding host genes

Basic information

Region (hg38): 19:11483426-11505839

Links

ENSG00000161914 ∙ NCBI:115950 ∙ OMIM:611371 ∙ HGNC:25196 ∙ Uniprot:Q96CK0 ∙ 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 ZNF653 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF653 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			41	4		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	41	5	0

Variants in ZNF653

This is a list of pathogenic ClinVar variants found in the ZNF653 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-11483686-G-C		not specified	Uncertain significance (Oct 03, 2022)
19-11483694-G-C		not specified	Uncertain significance (Dec 15, 2022)
19-11483701-G-A		not specified	Uncertain significance (Sep 20, 2023)
19-11483702-G-A		not specified	Uncertain significance (Aug 22, 2022)
19-11483702-G-C		not specified	Uncertain significance (Feb 17, 2024)
19-11483762-G-A		not specified	Uncertain significance (Sep 28, 2022)
19-11483786-C-T		not specified	Uncertain significance (Oct 06, 2022)
19-11483833-C-T		not specified	Uncertain significance (Jan 30, 2024)
19-11485739-T-C		not specified	Uncertain significance (Nov 17, 2022)
19-11486857-C-T		not specified	Uncertain significance (Oct 22, 2021)
19-11487081-C-T		not specified	Uncertain significance (Jun 10, 2024)
19-11487089-G-A		not specified	Uncertain significance (Apr 05, 2023)
19-11487123-T-C		not specified	Uncertain significance (May 11, 2022)
19-11487132-T-C		not specified	Uncertain significance (Sep 20, 2023)
19-11487143-C-T		not specified	Likely benign (Jul 19, 2022)
19-11487318-G-A		not specified	Uncertain significance (Aug 10, 2021)
19-11487331-T-C		not specified	Uncertain significance (Oct 03, 2022)
19-11487473-G-C			Likely benign (Dec 01, 2022)
19-11487493-C-T		not specified	Uncertain significance (Apr 04, 2023)
19-11487577-C-T		not specified	Likely benign (Feb 09, 2023)
19-11487592-C-T		not specified	Likely benign (Jan 24, 2024)
19-11487700-C-A		not specified	Uncertain significance (Jun 23, 2023)
19-11487712-C-T			Likely benign (Dec 01, 2022)
19-11487721-C-T		not specified	Uncertain significance (Nov 09, 2021)
19-11487760-C-T		not specified	Uncertain significance (Aug 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF653	protein_coding	protein_coding	ENST00000293771	9	22497

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00129	0.997	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.67	289	380	0.760	0.0000255	3930
Missense in Polyphen		72	129.59	0.55558		1239
Synonymous	-1.56	196	170	1.15	0.0000135	1245
Loss of Function	2.76	9	23.4	0.384	0.00000100	289

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000122	0.000121
Ashkenazi Jewish	0.00	0.00
East Asian	0.000168	0.000163
Finnish	0.0000566	0.0000462
European (Non-Finnish)	0.0000653	0.0000615
Middle Eastern	0.000168	0.000163
South Asian	0.0000335	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor. May repress NR5A1, PPARG, NR1H3, NR4A2, ESR1 and NR3C1 transcriptional activity. {ECO:0000269|PubMed:12920234}.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.398
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.57

Haploinsufficiency Scores

• pHI: 0.269
• hipred: Y
• hipred_score: 0.656
• ghis: 0.614

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.907

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp653

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;extracellular negative regulation of signal transduction;negative regulation of nucleic acid-templated transcription
• Cellular component: cellular_component;extracellular region;nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;transcription corepressor activity;transcription factor binding;metal ion binding;receptor antagonist activity;AF-2 domain binding