ZBTB1

zinc finger and BTB domain containing 1, the group of BTB domain containing|Zinc fingers C2H2-type

Basic information

Region (hg38): 14:64503712-64533690

Links

ENSG00000126804 ∙ NCBI:22890 ∙ OMIM:616578 ∙ HGNC:20259 ∙ Uniprot:Q9Y2K1 ∙ 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 ZBTB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZBTB1 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			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	1	0

Variants in ZBTB1

This is a list of pathogenic ClinVar variants found in the ZBTB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-64522130-C-T		not specified	Uncertain significance (Nov 09, 2022)
14-64522243-A-T		not specified	Uncertain significance (Oct 12, 2021)
14-64522309-G-A		not specified	Likely benign (Nov 27, 2023)
14-64522330-A-T		not specified	Uncertain significance (Mar 20, 2024)
14-64522403-G-A		not specified	Uncertain significance (May 03, 2023)
14-64522444-G-A		not specified	Uncertain significance (Apr 07, 2022)
14-64522452-A-C		not specified	Uncertain significance (Sep 20, 2023)
14-64522505-T-C		not specified	Uncertain significance (Feb 22, 2023)
14-64522537-A-G		not specified	Uncertain significance (Apr 22, 2022)
14-64522570-A-C		not specified	Uncertain significance (Dec 12, 2023)
14-64522676-G-A		not specified	Uncertain significance (Sep 23, 2023)
14-64522701-A-T		not specified	Uncertain significance (Dec 26, 2023)
14-64522754-A-G		not specified	Uncertain significance (Dec 28, 2022)
14-64522776-G-C		not specified	Uncertain significance (May 22, 2023)
14-64522790-C-A		not specified	Uncertain significance (Mar 04, 2024)
14-64522790-C-G		not specified	Uncertain significance (Mar 01, 2024)
14-64522810-T-C		not specified	Uncertain significance (Sep 20, 2023)
14-64522955-C-A		not specified	Uncertain significance (Jan 23, 2024)
14-64523009-A-G		not specified	Uncertain significance (Sep 29, 2022)
14-64523010-T-G		not specified	Uncertain significance (Apr 27, 2024)
14-64523013-G-A		not specified	Uncertain significance (Oct 26, 2021)
14-64523014-T-G		not specified	Uncertain significance (Sep 26, 2023)
14-64523129-G-A		not specified	Uncertain significance (Apr 01, 2024)
14-64523144-A-G		not specified	Uncertain significance (Aug 16, 2021)
14-64523488-A-G		not specified	Uncertain significance (Apr 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZBTB1	protein_coding	protein_coding	ENST00000394712	1	29979

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.994	0.00593	125735	0	7	125742	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.97	211	372	0.567	0.0000185	4833
Missense in Polyphen		60	152.48	0.39349		2039
Synonymous	1.99	99	128	0.776	0.00000620	1224
Loss of Function	4.17	2	24.1	0.0831	0.00000151	316

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional repressor (PubMed:20797634). Represses cAMP-responsive element (CRE)-mediated transcriptional activation (PubMed:21706167). In addition, has a role in translesion DNA synthesis. Requires for UV-inducible RAD18 loading, PCNA monoubiquitination, POLH recruitment to replication factories and efficient translesion DNA synthesis (PubMed:24657165). Plays a key role in the transcriptional regulation of T lymphocyte development (By similarity). {ECO:0000250|UniProtKB:Q91VL9, ECO:0000269|PubMed:20797634, ECO:0000269|PubMed:21706167, ECO:0000269|PubMed:24657165}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.476
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.99

Haploinsufficiency Scores

• pHI: 0.463
• hipred: Y
• hipred_score: 0.732
• ghis: 0.610

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.746

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zbtb1
• Phenotype: immune system phenotype; hematopoietic system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;positive regulation of T cell mediated immunity;DNA repair;chromatin remodeling;cellular response to DNA damage stimulus;translesion synthesis;B cell differentiation;positive regulation of natural killer cell differentiation;T cell differentiation in thymus;cellular response to UV;mRNA transcription by RNA polymerase II;innate immune response;positive regulation of T cell differentiation;thymus development;protein homooligomerization;positive regulation of pro-T cell differentiation
• Cellular component: nucleus;nucleoplasm;nuclear body;nuclear membrane
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;protein homodimerization activity;metal ion binding;protein heterodimerization activity;K63-linked polyubiquitin modification-dependent protein binding