ZBTB4

zinc finger and BTB domain containing 4, the group of BTB domain containing|Zinc fingers C2H2-type

Basic information

Region (hg38): 17:7459365-7484263

Links

ENSG00000174282 ∙ NCBI:57659 ∙ OMIM:612308 ∙ HGNC:23847 ∙ Uniprot:Q9P1Z0 ∙ 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 ZBTB4 gene.

• Inborn genetic diseases (69 variants)
• not provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZBTB4 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	5	7
missense			42	5	3	50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			20	2		22
Total	0	0	62	9	8

Variants in ZBTB4

This is a list of pathogenic ClinVar variants found in the ZBTB4 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7461952-G-A			Likely benign (Apr 01, 2023)
17-7461988-T-G		not specified	Uncertain significance (Mar 14, 2024)
17-7462044-C-T		not specified	Likely benign (Jul 14, 2021)
17-7462050-G-A		not specified	Uncertain significance (Mar 07, 2023)
17-7462071-C-T		not specified	Uncertain significance (Feb 13, 2023)
17-7462072-G-A			Benign (Apr 09, 2018)
17-7462089-G-A		not specified	Uncertain significance (Sep 06, 2022)
17-7462152-G-C		not specified	Uncertain significance (Nov 17, 2023)
17-7462185-C-T		not specified	Uncertain significance (Mar 21, 2022)
17-7462200-G-A		not specified	Uncertain significance (Nov 21, 2022)
17-7462209-C-T		not specified	Uncertain significance (Feb 28, 2024)
17-7462263-T-C		not specified	Uncertain significance (Jun 09, 2022)
17-7462265-C-T			Benign (Jun 26, 2018)
17-7462332-G-A		not specified	Uncertain significance (Nov 07, 2022)
17-7462335-C-T		not specified	Uncertain significance (Jan 03, 2024)
17-7462343-A-G		not specified	Uncertain significance (Oct 05, 2022)
17-7462359-A-G		not specified	Uncertain significance (Jun 16, 2023)
17-7462382-T-C		not specified	Uncertain significance (Jul 26, 2022)
17-7462392-C-T		not specified	Uncertain significance (Apr 10, 2023)
17-7462455-C-T		not specified	Uncertain significance (Apr 28, 2022)
17-7462482-C-T		not specified	Uncertain significance (Jan 17, 2024)
17-7462544-T-C		not specified	Uncertain significance (Feb 01, 2023)
17-7462710-C-T		not specified	Uncertain significance (Aug 29, 2022)
17-7462734-C-G		not specified	Uncertain significance (Nov 06, 2023)
17-7462737-C-T		not specified	Likely benign (Jan 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZBTB4	protein_coding	protein_coding	ENST00000311403	2	24898

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000940	125735	0	12	125747	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.93	498	635	0.784	0.0000398	6299
Missense in Polyphen		88	131.28	0.6703		1280
Synonymous	-0.338	278	271	1.03	0.0000179	2344
Loss of Function	4.76	0	26.3	0.00	0.00000156	287

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000526	0.0000462
European (Non-Finnish)	0.0000629	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000656	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor with bimodal DNA-binding specificity. Represses transcription in a methyl-CpG-dependent manner. Binds with a higher affinity to methylated CpG dinucleotides in the consensus sequence 5'-CGCG-3' but can also bind to the non-methylated consensus sequence 5'-CTGCNA-3' also known as the consensus kaiso binding site (KBS). Can also bind specifically to a single methyl-CpG pair and can bind hemimethylated DNA but with a lower affinity compared to methylated DNA (PubMed:16354688). Plays a role in postnatal myogenesis, may be involved in the regulation of satellite cells self-renewal (By similarity). {ECO:0000250|UniProtKB:Q5F293, ECO:0000269|PubMed:16354688}.

Recessive Scores

• pRec: 0.0822

Intolerance Scores

• loftool: 0.220
• rvis_EVS: -0.1
• rvis_percentile_EVS: 45.65

Haploinsufficiency Scores

• pHI: 0.378
• hipred: Y
• hipred_score: 0.572
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.996

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zbtb4
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); vision/eye phenotype

Zebrafish Information Network

• Gene name: zbtb4
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: curved dorsal

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription, DNA-templated;cellular response to DNA damage stimulus;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;nucleoplasm;chromosome;cytosol;nuclear body
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding;methyl-CpG binding;methyl-CpNpG binding;protein kinase binding;protein homodimerization activity;sequence-specific DNA binding;metal ion binding