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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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PGBD1
piggyBac transposable element derived 1
Chromosome 6 · 6p22.1
NCBI Gene: 84547Ensembl: ENSG00000137338.7HGNC: HGNC:19398UniProt: Q96JS3
26PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
neurogenesisnucleusprotein bindingidentical protein bindingIsolated anophthalmia - microphthalmiamicrophthalmiananophthalmiaisolated microphthalmia 7
✦AI Summary

PGBD1 is a mammal-specific domesticated transposase derived from piggyBac DNA transposons that has lost transposition activity but retained DNA-binding capability 1. Although the gene body retains much of the original transposon sequence and has captured SCAN and KRAB domains, PGBD1 no longer recognizes piggyBac inverted repeats 1. Genome-scale analysis reveals enriched binding sites in and around genes involved in neuronal development, with associations to both histone activating and repressing marks 1. PGBD1 specifically binds the promoter and gene body of NEAT1, a long noncoding RNA encoding the core structural component of neuronal paraspeckles 1. PGBD1 depletion in neuronal progenitor cells increases NEAT1 expression and paraspeckle formation, impairing cellular differentiation 1. This suggests PGBD1 evolved core regulatory functions maintaining neural progenitor cell identity. Regarding disease relevance, PGBD1 has been implicated in schizophrenia susceptibility through genome-wide association studies, with polymorphisms at chromosome 6-p22.1 showing significant association in multiple populations 23. Additionally, PGBD1 variants show suggestive association with age-at-onset in late-onset Alzheimer's disease 4. The gene represents a rare example of evolutionary acquisition of novel function coupled with emergence of a mammal-specific cellular structure.

Sources cited
1
PGBD1 is mammal-specific, has lost transposase activity but retained DNA-binding capability, binds neuronal development genes and NEAT1, suppresses paraspeckle assembly, and maintains neural progenitor cell identity
PMID: 36205081
2
PGBD1 polymorphisms at chromosome 6p21-p22.1 are associated with schizophrenia in Chinese Han population
PMID: 23437227
3
PGBD1 genetic variants are implicated in schizophrenia based on GWAS findings
PMID: 31096178
4
PGBD1 shows suggestive association with age-at-onset of late-onset Alzheimer's disease
PMID: 21132329
5
PGBD1 represents a less consistently replicated GWAS signal in Alzheimer's disease compared to other loci
PMID: 19808789
6
PGBD1 associations with schizophrenia in Japanese population were not sustained in replication studies
PMID: 22488895
Disease Associationsⓘ20
Isolated anophthalmia - microphthalmiaOpen Targets
0.08Suggestive
microphthalmiaOpen Targets
0.08Suggestive
nanophthalmiaOpen Targets
0.06Suggestive
isolated microphthalmia 7Open Targets
0.06Suggestive
nanophthalmos 2Open Targets
0.06Suggestive
Microphthalmia - ankyloblepharon - intellectual disabilityOpen Targets
0.06Suggestive
Testicular regression syndromeOpen Targets
0.05Suggestive
Alzheimer diseaseOpen Targets
0.05Suggestive
microphthalmia, isolated, with coloboma 10Open Targets
0.03Suggestive
46,XX ovotesticular disorder of sex developmentOpen Targets
0.03Suggestive
Leydig cell hypoplasiaOpen Targets
0.03Suggestive
testicular agenesisOpen Targets
0.03Suggestive
46,XY partial gonadal dysgenesisOpen Targets
0.03Suggestive
46,XY sex reversal 11Open Targets
0.03Suggestive
microphthalmia, isolated, with coloboma 5Open Targets
0.03Suggestive
Meacham syndromeOpen Targets
0.03Suggestive
Mayer-Rokitansky-Kuster-Hauser syndromeOpen Targets
0.03Suggestive
Mayer-Rokitansky-Küster-Hauser syndromeOpen Targets
0.03Suggestive
Mayer-Rokitansky-Kuster-Hauser syndrome type 1Open Targets
0.03Suggestive
congenital adrenal hyperplasia due to 11-beta-hydroxylase deficiencyOpen Targets
0.03Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
BTBD1Shared pathway100%BTBD2Shared pathway100%BTBD6Shared pathway100%ZKSCAN4Protein interaction84%SCAND1Protein interaction84%ZNF446Protein interaction84%
Tissue Expression6 tissues
Brain
100%
Ovary
78%
Bone Marrow
77%
Heart
70%
Liver
59%
Lung
53%
Gene Interaction Network
Click a node to explore
PGBD1BTBD1BTBD2BTBD6ZKSCAN4SCAND1ZNF446
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q96JS3
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
1.02LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.73 [0.53–1.02]
RankingsWhere PGBD1 stands among ~20K protein-coding genes
  • #12,846of 20,598
    Most Researched26
  • #9,955of 17,882
    Most Constrained (LOEUF)1.02
Genes detectedPGBD1
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
A Novel Gene Controls a New Structure: PiggyBac Transposable Element-Derived 1, Unique to Mammals, Controls Mammal-Specific Neuronal Paraspeckles.
PMID: 36205081
Mol Biol Evol · 2022
1.00
2
Unravelling the genetic basis of schizophrenia and bipolar disorder with GWAS: A systematic review.
PMID: 31096178
J Psychiatr Res · 2019
0.90
3
Chromosome 6p SNP microhaplotypes and IgG3 levels in hemochromatosis probands with HFE p.C282Y homozygosity.
PMID: 32623342
Blood Cells Mol Dis · 2020
0.80
4
Replication of association between schizophrenia and chromosome 6p21-6p22.1 polymorphisms in Chinese Han population.
PMID: 23437227
PLoS One · 2013
0.70
5
Investigation of 15 of the top candidate genes for late-onset Alzheimer's disease.
PMID: 21132329
Hum Genet · 2011
0.60