ZFP3

ZFP3 zinc finger protein, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 17:5078467-5096374

Links

ENSG00000180787 ∙ NCBI:124961 ∙ OMIM:194480 ∙ HGNC:12861 ∙ Uniprot:Q96NJ6 ∙ 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 ZFP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZFP3 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in ZFP3

This is a list of pathogenic ClinVar variants found in the ZFP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-5091514-G-A		not specified	Uncertain significance (Jun 26, 2023)
17-5091610-C-T		not specified	Uncertain significance (May 21, 2024)
17-5091671-A-G		not specified	Uncertain significance (Apr 09, 2024)
17-5091730-T-C		not specified	Uncertain significance (Sep 27, 2022)
17-5091739-T-C		not specified	Uncertain significance (Jan 24, 2023)
17-5091838-G-A		not specified	Uncertain significance (Mar 15, 2024)
17-5091860-G-C		not specified	Uncertain significance (Aug 22, 2022)
17-5091887-C-T		not specified	Uncertain significance (Dec 08, 2023)
17-5091902-G-C		not specified	Uncertain significance (May 03, 2023)
17-5091967-C-T		not specified	Uncertain significance (Jun 28, 2023)
17-5092058-G-A		not specified	Uncertain significance (Dec 01, 2022)
17-5092151-A-G		not specified	Uncertain significance (May 20, 2024)
17-5092187-A-C		not specified	Uncertain significance (Jun 17, 2022)
17-5092227-T-G		not specified	Uncertain significance (Apr 18, 2023)
17-5092358-A-T		not specified	Uncertain significance (Apr 07, 2022)
17-5092436-G-A		not specified	Uncertain significance (Jun 07, 2024)
17-5092522-A-C		not specified	Uncertain significance (Dec 06, 2021)
17-5092718-C-T		not specified	Uncertain significance (Dec 02, 2022)
17-5092726-C-T		not specified	Uncertain significance (Jul 25, 2023)
17-5092799-A-G		not specified	Uncertain significance (Oct 12, 2021)
17-5092886-A-G		not specified	Uncertain significance (Dec 17, 2023)
17-5092967-G-A		not specified	Uncertain significance (Oct 22, 2021)
17-5092976-A-G		not specified	Uncertain significance (Sep 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZFP3	protein_coding	protein_coding	ENST00000318833	1	18127

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00143	0.969	125729	0	18	125747	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.49	197	265	0.743	0.0000126	3362
Missense in Polyphen		56	113.83	0.49196		1442
Synonymous	0.117	89	90.4	0.984	0.00000414	886
Loss of Function	1.91	7	15.0	0.467	6.91e-7	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.611
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.260
• hipred: N
• hipred_score: 0.131
• ghis: 0.561

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.666

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zfp3

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;biological_process
• Cellular component: cellular_component;nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;molecular_function;DNA binding;metal ion binding