ZBTB7A

protein-coding

zinc finger and BTB domain containing 7A, the group of Zinc fingers C2H2-type|BTB domain containing

Gene summary

Enables several functions, including DNA-binding transcription factor activity; nuclear androgen receptor binding activity; and transcription corepressor binding activity. Involved in several processes, including erythrocyte maturation; negative regulation of signal transduction; and regulation of RNA metabolic process. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:
  • ZBTB7

MANE transcript

NM_015898.4

Inheritance

AD

ClinVar variants

P:24U:116B:33

Top phenotype

Macrocephaly, neurodevelopmental delay, lymphoid hyperplasia, and persistent fetal hemoglobin

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr19:4,043,303-4,066,899

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~23.6 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

macrocephaly, neurodevelopmental delay, lymphoid hyperplasia, and persistent fetal hemoglobinMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0859231

Submitter: G2P

macrocephaly, neurodevelopmental delay, lymphoid hyperplasia, and persistent fetal hemoglobinSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0859231

Submitter: PanelApp Australia

complex neurodevelopmental disorderSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0100038

Submitter: Ambry Genetics

macrocephaly, neurodevelopmental delay, lymphoid hyperplasia, and persistent fetal hemoglobinSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0859231

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Macrocephaly, neurodevelopmental delay, lymphoid hyperplasia, and persistent fetal hemoglobinAD

Manifestation: Allergy/Immunology/Infectious; Cardiovascular; Craniofacial; Hematologic; Neurologic

Intervention: Allergy/Immunology/Infectious; Cardiovascular

Rationale: The condition may involve congenital heart anomalies, some of which may require surgical and other interventions, and awareness may allow early diagnosis and management; Individuals may have sleep apnea due to lymphoid hypertrophy or adenoid overgrowth, and awareness may allow surgical and other interventions to manage this issue

Refs: 31645653; 34515416Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZBTB7A variants in ClinVar

8 Conditions Cataloged
not providedTotal: 69
Inborn genetic diseasesTotal: 69
Macrocephaly, neurodevelopmental delay, lymphoid hyperplasia, and persistent fetal hemoglobinTotal: 23
ZBTB7A-related disorderTotal: 16
not specifiedTotal: 14
Hereditary persistence of fetal hemoglobin-beta-thalassemia syndromeTotal: 3
Neurodevelopmental delayTotal: 1
Intellectual disability, autosomal dominant 29Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015898.4. 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
26
clinvar
26
missense
3
clinvar
1
clinvar
107
clinvar
7
clinvar
118
nonsense
3
clinvar
4
clinvar
2
clinvar
9
start loss
0
frameshift
7
clinvar
6
clinvar
6
clinvar
19
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total1311116330173

Highest pathogenic variant AF is 0.000007729561

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_015898.4RefSeqNP_056982.12MANE Select
ENST00000322357.9EnsemblENSP00000323670.32MANE Select
NM_001317990.2RefSeqNP_001304919.12Standard
ENST00000601588.1EnsemblENSP00000471865.12Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • b cell survival pathway

Biological Process

  • negative regulation of transcription by RNA polymerase II
  • regulation of alternative mRNA splicing, via spliceosome
  • regulation of glycolytic process
  • chromatin organization
  • chromatin remodeling

Molecular Function

  • RNA polymerase II proximal promoter sequence-specific DNA binding
  • DNA-binding transcription factor activity, RNA polymerase II-specific
  • transcription corepressor binding
  • DNA binding
  • DNA-binding transcription factor activity

Cellular Component

  • nucleus
  • cytoplasm
  • NuRD complex
  • site of double-strand break
  • DNA-dependent protein kinase complex

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000322357
Coding exons
2
Length
22582
Individuals with no LoFs
122864
Homozygous LoFs
0
Heterozygous LoFs
2
Defined
122866
p
0.00000814
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense4.041754040.4340.00003193733
Missense (PolyPhen)27132.660.203521137
Synonymous1.891702040.8320.00002031187
Loss of Function3.27114.40.06947.90e-7150

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish0.0000490.000049rare
European (Non-Finnish)0.00000910.0000091rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Transcription factor that represses the transcription of a wide range of genes involved in cell proliferation and differentiation (PubMed:14701838, PubMed:17595526, PubMed:20812024, PubMed:25514493, PubMed:26455326, PubMed:26816381). Directly and specifically binds to the consensus sequence 5'-[GA][CA]GACCCCCCCCC-3' and represses transcription both by regulating the organization of chromatin and through the direct recruitment of transcription factors to gene regulatory regions (PubMed:12004059, PubMed:17595526, PubMed:20812024, PubMed:25514493, PubMed:26816381). Negatively regulates SMAD4 transcriptional activity in the TGF-beta signaling pathway through these two mechanisms (PubMed:25514493). That is, recruits the chromatin regulator HDAC1 to the SMAD4-DNA complex and in parallel prevents the recruitment of the transcriptional activators CREBBP and EP300 (PubMed:25514493). Collaborates with transcription factors like RELA to modify the accessibility of gene transcription regulatory regions to secondary transcription factors (By similarity). Also directly interacts with transcription factors like SP1 to prevent their binding to DNA (PubMed:12004059). Functions as an androgen receptor/AR transcriptional corepressor by recruiting NCOR1 and NCOR2 to the androgen response elements/ARE on target genes (PubMed:20812024). Thereby, negatively regulates androgen receptor signaling and androgen-induced cell proliferation (PubMed:20812024). Involved in the switch between fetal and adult globin expression during erythroid cells maturation (PubMed:26816381). Through its interaction with the NuRD complex regulates chromatin at the fetal globin genes to repress their transcription (PubMed:26816381). Specifically represses the transcription of the tumor suppressor ARF isoform from the CDKN2A gene (By similarity). Efficiently abrogates E2F1-dependent CDKN2A transactivation (By similarity). Regulates chondrogenesis through the transcriptional repression of specific genes via a mechanism that also requires histone deacetylation (By similarity). Regulates cell proliferation through the transcriptional regulation of genes involved in glycolysis (PubMed:26455326). Involved in adipogenesis through the regulation of genes involved in adipocyte differentiation (PubMed:14701838). Plays a key role in the differentiation of lymphoid progenitors into B and T lineages (By similarity). Promotes differentiation towards the B lineage by inhibiting the T-cell instructive Notch signaling pathway through the specific transcriptional repression of Notch downstream target genes (By similarity). Also regulates osteoclast differentiation (By similarity). May also play a role, independently of its transcriptional activity, in double-strand break repair via classical non-homologous end joining/cNHEJ (By similarity). Recruited to double-strand break sites on damage DNA, interacts with the DNA-dependent protein kinase complex and directly regulates its stability and activity in DNA repair (By similarity). May also modulate the splicing activity of KHDRBS1 toward BCL2L1 in a mechanism which is histone deacetylase- dependent and thereby negatively regulates the pro-apoptotic effect of KHDRBS1 (PubMed:24514149). {ECO:0000250|UniProtKB:O88939, ECO:0000250|UniProtKB:Q9QZ48, ECO:0000269|PubMed:12004059, ECO:0000269|PubMed:14701838, ECO:0000269|PubMed:17595526, ECO:0000269|PubMed:20812024, ECO:0000269|PubMed:24514149, ECO:0000269|PubMed:25514493, ECO:0000269|PubMed:26455326, ECO:0000269|PubMed:26816381}.;

Recessive Scores

pRec
0.147

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
S
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
1.00

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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