GeneBe

ZBTB16

protein-coding

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

Gene summary

This gene is a member of the Krueppel C2H2-type zinc-finger protein family and encodes a zinc finger transcription factor that contains nine Kruppel-type zinc finger domains at the carboxyl terminus. This protein is located in the nucleus, is involved in cell cycle progression, and interacts with a histone deacetylase. Specific instances of aberrant gene rearrangement at this locus have been associated with acute promyelocytic leukemia (APL). Alternate transcriptional splice variants have been characterized. [provided by RefSeq, Jul 2008]

Previous symbols:
  • ZNF145

MANE transcript

NM_006006.6

Inheritance

AR

ClinVar variants

U:74B:31

Top phenotype

Skeletal defects, genital hypoplasia, and mental retardation

gnomAD constraint

pLI —, LoF o/e 0.04

Max pathogenic AF

—

Genomic locus

chr11:114,059,041-114,256,765

External References & Databases

Ensembl (ENSG00000109906)NCBI Gene (7704)OMIM (176797)HGNC:12930GenCCUniProt (Q05516)AlphaFoldClinVar (ZBTB16)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~197.7 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

skeletal defects, genital hypoplasia, and impaired intellectual developmentMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0012909

Submitter: PanelApp Australia

skeletal defects, genital hypoplasia, and impaired intellectual developmentLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0012909

Submitter: G2P

skeletal defects, genital hypoplasia, and impaired intellectual developmentLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0012909

Submitter: Ambry Genetics

skeletal defects, genital hypoplasia, and impaired intellectual developmentLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0012909

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Skeletal defects, genital hypoplasia, and mental retardationAR

Manifestation: Genitourinary; Musculoskeletal; Neurologic

Intervention: General

Rationale: 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

Refs: 11891687; 18611983Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZBTB16 variants in ClinVar

5 Conditions Cataloged
not specifiedTotal: 69
not providedTotal: 25
ZBTB16-related disorderTotal: 7
Skeletal defects, genital hypoplasia, and intellectual disabilityTotal: 1
See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006006.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
25
clinvar
2
clinvar
 29
missense
69
clinvar
4
clinvar
 73
nonsense
2
clinvar
 2
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
 1
Total0074292105
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 107 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_006006.6RefSeqNP_005997.26MANE Select
ENST00000335953.9EnsemblENSP00000338157.46MANE Select
NM_001018011.3RefSeqNP_001018011.16Standard
NM_001354750.2RefSeqNP_001341679.16Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • 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

Biological Process

  • negative regulation of transcription by RNA polymerase II
  • mesonephros development
  • apoptotic process
  • central nervous system development
  • negative regulation of cell population proliferation

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

Cellular Component

  • nucleus
  • nucleoplasm
  • cytosol
  • plasma membrane
  • nuclear body

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000335953
Coding exons
6
Length
191084
Individuals with no LoFs
125743
Homozygous LoFs
0
Heterozygous LoFs
4
Defined
125747
p
0.0000159
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.472644040.6540.00002664443
Missense (PolyPhen)47160.550.292741765
Synonymous-0.5091841751.050.00001311316
Loss of Function4.41124.60.04060.00000132287

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000180.000018rare
South Asian00.0absent
Other0.000160.00016rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec
0.501

Intolerance Scores

LoFtool
0.115
RVIS EVS
-0.8
RVIS percentile EVS
12.33

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.995

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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