ZNF3

zinc finger protein 3, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 7:100064033-100082548

Links

ENSG00000166526 ∙ NCBI:7551 ∙ OMIM:194510 ∙ HGNC:13089 ∙ Uniprot:P17036 ∙ 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 ZNF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZNF3 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			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			11	1		12
Total	0	0	25	2	0

Variants in ZNF3

This is a list of pathogenic ClinVar variants found in the ZNF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-100064040-G-C		not specified	Uncertain significance (Apr 25, 2023)
7-100064058-A-G		not specified	Uncertain significance (Jan 08, 2024)
7-100064060-A-G		not specified	Uncertain significance (Jun 24, 2022)
7-100064085-G-C		not specified	Uncertain significance (Sep 16, 2021)
7-100064123-T-C		not specified	Uncertain significance (Feb 27, 2024)
7-100064208-G-T		not specified	Uncertain significance (Jun 10, 2022)
7-100064250-G-A		not specified	Uncertain significance (Aug 10, 2021)
7-100064442-A-G		not specified	Uncertain significance (Apr 25, 2022)
7-100064472-A-C		not specified	Uncertain significance (Oct 16, 2023)
7-100064511-C-T		not specified	Uncertain significance (Dec 13, 2023)
7-100064562-A-G		not specified	Uncertain significance (Dec 22, 2023)
7-100064613-C-T		not specified	Likely benign (Oct 10, 2023)
7-100071174-G-A		not specified	Uncertain significance (Jan 16, 2024)
7-100071561-C-A		not specified	Uncertain significance (Mar 29, 2024)
7-100071612-T-A		not specified	Uncertain significance (Apr 22, 2024)
7-100071624-T-C		not specified	Uncertain significance (Aug 17, 2022)
7-100071841-G-A		not specified	Uncertain significance (Oct 12, 2021)
7-100071885-T-C		not specified	Uncertain significance (Jun 11, 2021)
7-100071942-A-C		not specified	Uncertain significance (Nov 30, 2021)
7-100071973-T-C		not specified	Uncertain significance (Dec 05, 2022)
7-100072050-C-T		not specified	Uncertain significance (Jul 15, 2021)
7-100072077-A-C		not specified	Uncertain significance (Dec 08, 2023)
7-100072089-C-T		not specified	Likely benign (Dec 28, 2022)
7-100072186-G-C		not specified	Uncertain significance (Jul 13, 2021)
7-100072187-A-T		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZNF3	protein_coding	protein_coding	ENST00000303915	4	18516

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000198	0.903	125563	0	20	125583	0.0000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.31	190	248	0.766	0.0000129	2971
Missense in Polyphen		62	94.884	0.65343		1200
Synonymous	0.199	96	98.5	0.974	0.00000572	820
Loss of Function	1.57	10	17.0	0.589	8.75e-7	224

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.0000544	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000795	0.0000792
Middle Eastern	0.0000544	0.0000544
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in cell differentiation and/or proliferation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.0949

Intolerance Scores

• loftool: 0.606
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.56

Haploinsufficiency Scores

• pHI: 0.509
• hipred: N
• hipred_score: 0.285
• ghis: 0.631

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.994

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp113

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;multicellular organism development;cell differentiation;leukocyte activation
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;zinc ion binding;identical protein binding