ZBTB3

zinc finger and BTB domain containing 3, the group of BTB domain containing|Zinc fingers C2H2-type

Basic information

Region (hg38): 11:62748319-62754184

Links

ENSG00000185670 ∙ NCBI:79842 ∙ ∙ HGNC:22918 ∙ Uniprot:Q9H5J0 ∙ 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 ZBTB3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZBTB3 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			30	3		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			3			3
Total	0	0	33	3	0

Variants in ZBTB3

This is a list of pathogenic ClinVar variants found in the ZBTB3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-62752164-T-C		not specified	Uncertain significance (May 28, 2024)
11-62752166-G-C		not specified	Uncertain significance (Aug 10, 2021)
11-62752196-A-T		not specified	Uncertain significance (Feb 14, 2025)
11-62752245-T-G		not specified	Uncertain significance (Jun 11, 2021)
11-62752366-G-C		not specified	Uncertain significance (Oct 16, 2024)
11-62752410-C-T		not specified	Uncertain significance (Dec 06, 2021)
11-62752482-C-T		not specified	Uncertain significance (May 12, 2024)
11-62752487-G-C		not specified	Uncertain significance (Nov 15, 2024)
11-62752559-G-T		not specified	Uncertain significance (Mar 25, 2024)
11-62752620-C-T		not specified	Uncertain significance (Apr 17, 2024)
11-62752632-C-G		not specified	Uncertain significance (Mar 15, 2024)
11-62752665-C-T		not specified	Uncertain significance (Oct 14, 2021)
11-62752689-G-C		not specified	Uncertain significance (Nov 15, 2024)
11-62752712-A-C		not specified	Uncertain significance (Mar 03, 2025)
11-62752715-T-C		not specified	Uncertain significance (Oct 06, 2021)
11-62752776-C-G		not specified	Uncertain significance (Jan 03, 2025)
11-62752829-G-A		not specified	Uncertain significance (Apr 22, 2022)
11-62752835-G-A		not specified	Uncertain significance (Sep 28, 2023)
11-62752845-G-T		not specified	Uncertain significance (Nov 18, 2022)
11-62752848-G-A		not specified	Uncertain significance (Nov 10, 2022)
11-62752977-G-A		not specified	Uncertain significance (Jan 24, 2025)
11-62752980-T-G		not specified	Uncertain significance (Feb 27, 2025)
11-62753042-C-T		not specified	Uncertain significance (Dec 28, 2022)
11-62753055-C-A		not specified	Likely benign (Sep 25, 2024)
11-62753055-C-T		not specified	Uncertain significance (Nov 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZBTB3	protein_coding	protein_coding	ENST00000394807	2	5870

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0193	0.977	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	274	329	0.832	0.0000183	3649
Missense in Polyphen		50	105.73	0.47291		1111
Synonymous	0.409	124	130	0.954	0.00000654	1285
Loss of Function	2.55	6	17.5	0.343	9.83e-7	197

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000868	0.0000868
Ashkenazi Jewish	0.000397	0.000397
East Asian	0.000218	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000795	0.0000791
Middle Eastern	0.000218	0.000217
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0867

Intolerance Scores

• loftool: 0.545
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.38

Haploinsufficiency Scores

• pHI: 0.525
• hipred: N
• hipred_score: 0.485
• ghis: 0.418

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.922

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zbtb3

Gene ontology

• Biological process: cellular response to DNA damage stimulus
• Cellular component: nucleus
• Molecular function: DNA binding;metal ion binding