PGBD3

Summary

PGBD3 (piggyBac transposable element derived 3, HGNC:19400) is a protein-coding gene on chromosome 10q11, encoding PiggyBac transposable element-derived protein 3 (Q8N328). Binds in vitro to PGBD3-related transposable elements, called MER85s; these non-autonomous 140 bp elements are characterized by the presence of PGBD3 terminal inverted repeats and the absence of internal transposase ORF.

This gene is a member of a small family of genes derived from piggyBac transposable elements. The encoded protein contains a zinc-ribbon domain characteristic of transposon-derived proteins and may function as a regulator of transcription. Alternative splicing occurs between a splice site from exon 5 of the adjacent upstream gene ’excision repair cross-complementation group 6’ (ERCC6, GeneID: 2074) and the 3’ splice site upstream of the open reading frame (ORF) of this gene, which activates the alternative polyadenylation site downstream of the piggyback-derived-3 ORF. The resulting transcripts encode a fusion protein that shares sequence with the product of each individual gene. Pseudogenes for this gene are defined on chromosomes 4, 5 and 12.

Source: NCBI Gene 267004 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 19 total — 1 pathogenic, 3 likely-pathogenic

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19400
Approved symbol	PGBD3
Name	piggyBac transposable element derived 3
Location	10q11
Locus type	gene with protein product
Status	Approved
Aliases	FLJ90201
Entrez	267004

Gene structure

Transcript identifiers

Ensembl transcripts: 0

RefSeq mRNA: 0 — MANE Select: None

Canonical transcript exons

None — 0 exons

Expression profiles

Top tissues by expression

0 total, by Bgee expression score (0-100, higher = more expressed):

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

20 targeting PGBD3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-7162-3P	99.89	68.16	1682
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-324-3P	99.26	66.31	1034
HSA-MIR-6797-3P	99.17	66.94	668
HSA-MIR-6830-5P	99.01	68.73	1884
HSA-MIR-4709-3P	98.88	68.04	1594
HSA-MIR-655-5P	98.74	65.93	888
HSA-MIR-4501	98.72	67.19	921
HSA-MIR-654-3P	98.38	67.61	905
HSA-MIR-561-5P	98.25	68.13	1365
HSA-MIR-660-5P	98.16	68.27	680
HSA-MIR-3664-3P	97.85	67.62	1452

Literature-anchored findings (GeneRIF, showing 2)

• a domesticated PiggyBac-like transposon PGBD3, residing within intron 5 of the CSB gene, functions as an alternative 3’ terminal exon (PMID:18369450)
• CSB-PGBD3 fusion protein is important in both health and disease, and could play a role in Cockayne syndrome. (PMID:22483866)

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

PiggyBac transposable element-derived protein 3 — Q8N328 (reviewed: Q8N328)

All UniProt accessions (0):

UniProt curated annotations — full annotation on UniProt →

Function. Binds in vitro to PGBD3-related transposable elements, called MER85s; these non-autonomous 140 bp elements are characterized by the presence of PGBD3 terminal inverted repeats and the absence of internal transposase ORF.

Subcellular location. Nucleus.

Tissue specificity. Expressed in heart and oocytes, but not in granulosa cells (at protein level).

Miscellaneous. PGBD3 gene is located within ERCC6 intron 5.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N328-1	PGBD3	yes
P0DP91-1	CSB-PGBD3

RefSeq proteins (0): (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029526	PGBD	Domain
IPR052638	PiggyBac_TE-derived	Family

Pfam: PF13843

UniProt features (8 total): sequence variant 3, region of interest 2, chain 1, compositionally biased region 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N328-F1	84.30	0.61

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 86

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 0 (showing top):

GO Biological Process (0):

GO Molecular Function (1): sequence-specific DNA binding (GO:0043565)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

3 interactions, top by confidence:

A	B	Type	Score
RBBP4	TNRC18	psi-mi:“MI:0914”(association)	0.530
PGBD3	HOXA11	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (7): PGBD3 (Affinity Capture-MS), PGBD3 (Affinity Capture-MS), PGBD3 (Affinity Capture-MS), PGBD3 (Negative Genetic), PGBD3 (Affinity Capture-MS), PGBD3 (Affinity Capture-MS), PGBD3 (Two-hybrid)

ESM2 similar proteins: A0A345BJN8, A4Z943, A4Z944, A4Z945, A6ZW78, B2RD01, B2RRL2, O60108, P0CF88, P0CF89, P0CF90, P0CF97, P10978, P19769, P21328, P21329, P28912, P28916, P28917, P34257, P35878, P37245, P37247, P49777, P51026, P75741, P76119, Q09575, Q0VBL1, Q17RP2, Q2HEW6, Q49AG3, Q4R6P1, Q4W5G0, Q53H47, Q6AZB8, Q6NT04, Q6P3X8, Q79CE8, Q7JQ07

Diamond homologs: F8VPZ5, P0DP91, Q03468, Q6P3X8, Q8N328, Q96JS3, A1YEP8, A1YEQ3, A1YEV9, A1YFW2, A1YFW6, A1YG26, A1YG48, A1YG60, A1YGJ4, A2T6E3, A2T6V8, A2T6W2, A2T712, A2T736, A2T7D2, A2T7D7, A2T7F4, A2T7L7, A2T812, A6QNZ0, A6QPT6, B2KFW1, O14709, O14771, O14978, O15535, O43309, O60304, O95125, P10073, P17022, P17028, P17029, P17040

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

19 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	3
Uncertain significance	8
Likely benign	6
Benign	1

Top pathogenic / likely-pathogenic (4)

Variant ID	HGVS	Classification
684951	GRCh37/hg19 10q11.22-11.23(chr10:49378356-51250418)x1	Pathogenic
1726063	NM_000124.4(ERCC6):c.1214_1215insCTGGCACTTTCTT (p.Lys405fs)	Likely pathogenic
4813802	NM_001277058.2(ERCC6):c.1600C>T (p.Gln534Ter)	Likely pathogenic
992645	GRCh37/hg19 10q11.22-11.23(chr10:46966535-51874356)x1	Likely pathogenic

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000298378 (10:49519561 A>G), RS1000348694 (10:49519244 T>C), RS1000573143 (10:49521554 T>C), RS1000574030 (10:49525362 T>A), RS1000665345 (10:49520596 T>C), RS1001777752 (10:49520137 G>A,C), RS1001831657 (10:49521335 C>T), RS1001962298 (10:49523106 T>C), RS1002296474 (10:49515189 G>A,C), RS1003419951 (10:49519450 T>C), RS1003472249 (10:49519196 C>T), RS1003624122 (10:49525659 A>C), RS1003793848 (10:49522965 G>T), RS1004526228 (10:49524146 T>C), RS1004530364 (10:49523794 A>G)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:133540, MIM:214150, MIM:278800

GenCC curated gene-disease

Mondo (3): Cockayne syndrome type 2 (MONDO:0019570), cerebrooculofacioskeletal syndrome 1 (MONDO:0008955), de Sanctis-Cacchione syndrome (MONDO:0010217)

Orphanet (3): Cockayne syndrome (Orphanet:191), Cockayne syndrome type 2 (Orphanet:90322), De Sanctis-Cacchione syndrome (Orphanet:1569)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C535992	De Sanctis-Cacchione syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases expression	2
Tetrachlorodibenzodioxin	increases expression	2
Valproic Acid	affects expression, decreases expression, decreases methylation	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression, increases expression	2
coumarin	increases phosphorylation	1
CGP 52608	increases reaction, affects binding	1
bisphenol S	affects cotreatment, decreases expression	1
Caffeine	decreases phosphorylation	1
Dexamethasone	affects cotreatment, decreases expression	1
Diethylhexyl Phthalate	affects cotreatment, affects expression	1
Formaldehyde	decreases expression	1
Colforsin	affects cotreatment, affects expression	1
Indomethacin	affects cotreatment, decreases expression	1
Methyl Methanesulfonate	increases expression	1
Quercetin	decreases expression	1
Dronabinol	decreases expression	1
Urethane	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, decreases expression	1
Cyclosporine	decreases expression	1
Aflatoxin B1	increases methylation	1
Aflatoxin M1	decreases expression	1
Uranium Compounds	increases expression	1
Antirheumatic Agents	increases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.