ZBTB16

zinc finger and BTB domain containing 16, the group of BTB domain containing|Zinc fingers C2H2-type

Basic information

Region (hg38): 11:114059041-114256765

Previous symbols: [ "ZNF145" ]

Links

ENSG00000109906 ∙ NCBI:7704 ∙ OMIM:176797 ∙ HGNC:12930 ∙ Uniprot:Q05516 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• skeletal defects, genital hypoplasia, and intellectual disability (Limited), mode of inheritance: AR
• skeletal defects, genital hypoplasia, and intellectual disability (Limited), mode of inheritance: AR
• skeletal defects, genital hypoplasia, and intellectual disability (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Skeletal defects, genital hypoplasia, and mental retardation	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary; Musculoskeletal; Neurologic	11891687; 18611983

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZBTB16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZBTB16 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				19	5	24
missense			26	3		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding				1		1
Total	0	0	26	23	5

Variants in ZBTB16

This is a list of pathogenic ClinVar variants found in the ZBTB16 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-114063331-C-T		ZBTB16-related disorder	Likely benign (Jul 30, 2019)
11-114063390-C-T			Likely benign (Apr 01, 2023)
11-114063507-C-T		ZBTB16-related disorder	Likely benign (Feb 21, 2019)
11-114063561-A-G			Likely benign (Jul 20, 2018)
11-114063699-G-A			Benign (Dec 31, 2019)
11-114063702-G-A			Likely benign (Jul 04, 2018)
11-114063714-C-T			Likely benign (Aug 01, 2022)
11-114063726-C-T			Benign/Likely benign (Dec 01, 2023)
11-114063742-C-T		not specified	Uncertain significance (Oct 25, 2023)
11-114063743-G-A		See cases • not specified	Uncertain significance (Jun 29, 2022)
11-114063757-C-G		not specified	Uncertain significance (Oct 26, 2022)
11-114063790-G-C		not specified	Uncertain significance (Mar 29, 2024)
11-114063829-C-T		not specified	Uncertain significance (Jan 02, 2024)
11-114063865-A-G		ZBTB16-related disorder	Likely benign (Apr 01, 2022)
11-114063890-G-A		not specified	Uncertain significance (Aug 10, 2021)
11-114063972-C-G			Benign (Dec 31, 2019)
11-114063972-C-T			Benign (Dec 31, 2019)
11-114063978-G-C		not specified	Uncertain significance (Jan 31, 2024)
11-114063983-C-T		not specified	Uncertain significance (Jun 16, 2024)
11-114064000-C-T		not specified	Uncertain significance (Feb 28, 2023)
11-114064004-A-G		not specified	Uncertain significance (Dec 06, 2021)
11-114064028-C-T		not specified	Uncertain significance (Nov 03, 2022)
11-114064056-C-T			Likely benign (Apr 10, 2018)
11-114064057-A-G		not specified	Likely benign (Dec 12, 2023)
11-114064072-G-A		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZBTB16	protein_coding	protein_coding	ENST00000335953	6	191084

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000931	125743	0	4	125747	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.47	264	404	0.654	0.0000266	4443
Missense in Polyphen		47	160.55	0.29274		1765
Synonymous	-0.509	184	175	1.05	0.0000131	1316
Loss of Function	4.41	1	24.6	0.0406	0.00000132	287

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000617	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional repressor (PubMed:24359566). May play a role in myeloid maturation and in the development and/or maintenance of other differentiated tissues. Probable substrate-recognition component of an E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins (PubMed:14528312). {ECO:0000269|PubMed:14528312, ECO:0000269|PubMed:24359566}.
• Disease: DISEASE: Skeletal defects, genital hypoplasia, and mental retardation (SGYMR) [MIM:612447]: A disorder characterized by mental retardation, craniofacial dysmorphism, microcephaly and short stature. Additional features include absence of the thumbs, hypoplasia of the radii and ulnae, additional vertebrae and ribs, retarded bone age and genital hypoplasia. {ECO:0000269|PubMed:18611983}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=A chromosomal aberration involving ZBTB16 may be a cause of acute promyelocytic leukemia (APL). Translocation t(11;17)(q32;q21) with RARA. {ECO:0000269|PubMed:8384553}.
• Pathway: Acute myeloid leukemia - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Ectoderm Differentiation;Wnt-beta-catenin Signaling Pathway in Leukemia;Development and heterogeneity of the ILC family;Post-translational protein modification;Metabolism of proteins;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Neddylation (Consensus)

Recessive Scores

• pRec: 0.501

Intolerance Scores

• loftool: 0.115
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.33

Haploinsufficiency Scores

• pHI: 0.808
• hipred: Y
• hipred_score: 0.831
• ghis: 0.564

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.995

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zbtb16
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; neoplasm; limbs/digits/tail phenotype; immune system phenotype; skeleton phenotype; hematopoietic system phenotype; reproductive system phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;mesonephros development;apoptotic process;central nervous system development;negative regulation of cell population proliferation;embryonic pattern specification;anterior/posterior pattern specification;protein ubiquitination;hemopoiesis;myeloid cell differentiation;positive regulation of chondrocyte differentiation;protein localization to nucleus;embryonic hindlimb morphogenesis;forelimb morphogenesis;embryonic digit morphogenesis;positive regulation of apoptotic process;post-translational protein modification;positive regulation of fat cell differentiation;negative regulation of myeloid cell differentiation;positive regulation of ossification;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;male germ-line stem cell asymmetric division;positive regulation of NK T cell differentiation;cartilage development;positive regulation of cartilage development
• Cellular component: nucleus;nucleoplasm;cytosol;plasma membrane;nuclear body;PML body;nuclear speck;transcriptional repressor complex;protein-containing complex
• Molecular function: RNA polymerase II distal enhancer 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;protein C-terminus binding;protein domain specific binding;identical protein binding;protein homodimerization activity;sequence-specific DNA binding;metal ion binding