ZNF202

zinc finger protein 202, the group of Zinc fingers C2H2-type|SCAN domain containing

Basic information

Region (hg38): 11:123723913-123741675

Links

ENSG00000166261 ∙ NCBI:7753 ∙ OMIM:603430 ∙ HGNC:12994 ∙ Uniprot:O95125 ∙ 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 ZNF202 gene.

• Inborn genetic diseases (19 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF202 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					2	2
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	2

Variants in ZNF202

This is a list of pathogenic ClinVar variants found in the ZNF202 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-123726079-G-A		not specified	Uncertain significance (Dec 19, 2022)
11-123726148-C-A		not specified	Uncertain significance (May 31, 2022)
11-123726171-C-A		not specified	Uncertain significance (Aug 08, 2022)
11-123726244-C-A		not specified	Uncertain significance (Jul 12, 2023)
11-123726266-C-T		not specified	Uncertain significance (Oct 26, 2022)
11-123726283-G-A		not specified	Uncertain significance (Jul 26, 2022)
11-123726292-C-T		not specified	Uncertain significance (May 27, 2022)
11-123726486-G-A			Benign (Oct 24, 2018)
11-123726610-T-G		not specified	Uncertain significance (Sep 23, 2023)
11-123726637-C-T		not specified	Uncertain significance (Jun 29, 2022)
11-123726869-C-G		not specified	Uncertain significance (Dec 17, 2021)
11-123726967-T-A		not specified	Uncertain significance (Feb 07, 2023)
11-123728142-C-A		not specified	Uncertain significance (Jan 30, 2024)
11-123728210-C-T		not specified	Uncertain significance (Sep 01, 2021)
11-123728235-C-T		not specified	Uncertain significance (Mar 06, 2023)
11-123729162-G-T		not specified	Uncertain significance (Oct 26, 2022)
11-123729200-C-T		not specified	Uncertain significance (Nov 02, 2023)
11-123729656-C-T		not specified	Uncertain significance (Jan 21, 2022)
11-123729668-G-A		not specified	Uncertain significance (Jul 06, 2021)
11-123729714-C-T		not specified	Uncertain significance (Apr 21, 2022)
11-123729722-G-A		not specified	Likely benign (Jan 18, 2022)
11-123729737-T-A		not specified	Uncertain significance (Apr 19, 2023)
11-123729762-G-A		not specified	Uncertain significance (Oct 04, 2022)
11-123729766-C-T			Benign (May 15, 2018)
11-123729815-T-C		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF202	protein_coding	protein_coding	ENST00000336139	6	17499

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.526	0.474	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.69	277	369	0.752	0.0000211	4240
Missense in Polyphen		94	159.17	0.59057		1859
Synonymous	-0.326	147	142	1.03	0.00000844	1245
Loss of Function	3.88	6	28.3	0.212	0.00000147	334

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000217	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.000217	0.000217
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor that binds to elements found predominantly in genes that participate in lipid metabolism. Among its targets are structural components of lipoprotein particles (apolipoproteins AIV, CIII, and E), enzymes involved in lipid processing (lipoprotein lipase, lecithin cholesteryl ester transferase), transporters involved in lipid homeostasis (ABCA1, ABCG1), and several genes involved in processes related to energy metabolism and vascular disease.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.338
• rvis_EVS: -0.2
• rvis_percentile_EVS: 39.11

Haploinsufficiency Scores

• pHI: 0.147
• hipred: N
• hipred_score: 0.359
• ghis: 0.572

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.639

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp202
• Phenotype: growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;lipid metabolic process
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;metal ion binding