ZBTB46

zinc finger and BTB domain containing 46, the group of Zinc fingers C2H2-type|BTB domain containing

Basic information

Region (hg38): 20:63743668-63832038

Previous symbols: [ "ZNF340", "BTBD4" ]

Links

ENSG00000130584 ∙ NCBI:140685 ∙ OMIM:614639 ∙ HGNC:16094 ∙ Uniprot:Q86UZ6 ∙ 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 ZBTB46 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZBTB46 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			52	1		53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	1	0

Variants in ZBTB46

This is a list of pathogenic ClinVar variants found in the ZBTB46 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-63746938-G-A		not specified	Uncertain significance (Feb 27, 2023)
20-63746941-A-G		not specified	Uncertain significance (Jan 24, 2025)
20-63746967-G-A		not specified	Uncertain significance (Sep 27, 2022)
20-63746982-C-T		not specified	Uncertain significance (Jun 26, 2023)
20-63747012-G-A		not specified	Uncertain significance (Sep 24, 2024)
20-63747052-C-T		not specified	Uncertain significance (Nov 15, 2024)
20-63747075-C-T		not specified	Uncertain significance (Jun 02, 2023)
20-63747082-C-A		not specified	Uncertain significance (Nov 03, 2023)
20-63747105-C-T		not specified	Uncertain significance (Oct 20, 2023)
20-63747106-C-T		not specified	Uncertain significance (Oct 09, 2024)
20-63747139-C-T		not specified	Uncertain significance (Jan 17, 2024)
20-63747142-C-T		not specified	Uncertain significance (Dec 02, 2022)
20-63747151-C-T		not specified	Uncertain significance (Feb 27, 2023)
20-63747169-C-T		not specified	Uncertain significance (Jan 01, 2024)
20-63747178-C-T		not specified	Uncertain significance (Jun 26, 2024)
20-63747180-C-T		not specified	Uncertain significance (Apr 19, 2023)
20-63747193-C-T		not specified	Uncertain significance (Feb 27, 2023)
20-63747213-C-T		not specified	Uncertain significance (Nov 22, 2023)
20-63747249-A-G		not specified	Uncertain significance (May 23, 2024)
20-63747258-C-T		not specified	Uncertain significance (Oct 11, 2024)
20-63747261-C-G		not specified	Uncertain significance (Jun 05, 2023)
20-63747279-T-C		Marfanoid habitus and intellectual disability	Uncertain significance (-)
20-63752819-T-C		not specified	Uncertain significance (Feb 01, 2025)
20-63752850-T-C		not specified	Uncertain significance (Sep 16, 2021)
20-63775692-G-A		not specified	Uncertain significance (Jan 23, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZBTB46	protein_coding	protein_coding	ENST00000245663	4	87579

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.809	0.191	125723	0	8	125731	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.24	287	415	0.691	0.0000296	3815
Missense in Polyphen		63	123.16	0.51152		1137
Synonymous	-1.35	232	207	1.12	0.0000177	1193
Loss of Function	3.68	4	23.0	0.174	0.00000159	210

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000109
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000272	0.0000264
Middle Eastern	0.000111	0.000109
South Asian	0.0000427	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Function as a transcriptional repressor for PRDM1. {ECO:0000250}.

Intolerance Scores

• loftool: 0.240
• rvis_EVS: -0.86
• rvis_percentile_EVS: 10.85

Haploinsufficiency Scores

• pHI: 0.265
• hipred: Y
• hipred_score: 0.806
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.765

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zbtb46
• Phenotype: normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;negative regulation of granulocyte differentiation;negative regulation of macrophage differentiation;negative regulation of monocyte differentiation;negative regulation of dendritic cell differentiation;positive regulation of dendritic cell differentiation
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;nucleic acid binding;metal ion binding