PGBD4

Summary

PGBD4 (piggyBac transposable element derived 4, HGNC:19401) is a protein-coding gene on chromosome 15q14, encoding PiggyBac transposable element-derived protein 4 (Q96DM1).

The piggyBac family of proteins, found in diverse animals, are transposases related to the transposase of the canonical piggyBac transposon from the moth, Trichoplusia ni. This family also includes genes in several genomes, including human, that appear to have been derived from the piggyBac transposons. This gene belongs to the subfamily of piggyBac transposable element derived (PGBD) genes. The PGBD proteins appear to be novel, with no obvious relationship to other transposases, or other known protein families.

Source: NCBI Gene 161779 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 63 total
• MANE Select transcript: NM_152595

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19401
Approved symbol	PGBD4
Name	piggyBac transposable element derived 4
Location	15q14
Locus type	gene with protein product
Status	Approved
Aliases	FLJ32638, FLJ37497
Ensembl gene	ENSG00000182405
Ensembl biotype	protein_coding
OMIM	621245
Entrez	161779

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000397766

RefSeq mRNA: 1 — MANE Select: NM_152595 NM_152595

CCDS: CCDS10033

Canonical transcript exons

ENST00000397766 — 1 exons

Exon	Start	End
ENSE00001294545	34102083	34108686

Expression profiles

Bgee: expression breadth ubiquitous, 158 present calls, max score 78.42.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.6182 / max 53.7968, expressed in 1429 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
145787	1.9113	841
145786	1.4886	940
145785	0.2182	81

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	78.42	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	73.54	gold quality
pancreatic ductal cell	CL:0002079	70.06	silver quality
ileal mucosa	UBERON:0000331	68.27	silver quality
stromal cell of endometrium	CL:0002255	67.24	gold quality
tibialis anterior	UBERON:0001385	67.20	silver quality
islet of Langerhans	UBERON:0000006	67.16	gold quality
cortical plate	UBERON:0005343	67.10	gold quality
monocyte	CL:0000576	65.94	gold quality
leukocyte	CL:0000738	65.73	gold quality
prefrontal cortex	UBERON:0000451	65.58	gold quality
vermiform appendix	UBERON:0001154	64.44	gold quality
granulocyte	CL:0000094	63.73	gold quality
primary visual cortex	UBERON:0002436	63.09	gold quality
medial globus pallidus	UBERON:0002477	63.03	silver quality
hindlimb stylopod muscle	UBERON:0004252	62.93	gold quality
amniotic fluid	UBERON:0000173	62.92	silver quality
Brodmann (1909) area 9	UBERON:0013540	62.88	gold quality
bone marrow cell	CL:0002092	62.87	gold quality
oviduct epithelium	UBERON:0004804	62.63	silver quality
lymph node	UBERON:0000029	62.38	gold quality
right lobe of liver	UBERON:0001114	62.00	gold quality
rectum	UBERON:0001052	61.66	gold quality
ganglionic eminence	UBERON:0004023	61.08	gold quality
pancreas	UBERON:0001264	61.01	gold quality
muscle of leg	UBERON:0001383	60.55	gold quality
smooth muscle tissue	UBERON:0001135	60.46	gold quality
deltoid	UBERON:0001476	60.36	gold quality
right uterine tube	UBERON:0001302	60.35	gold quality
ventricular zone	UBERON:0003053	60.32	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-MTAB-6142	no	40.27
E-GEOD-99795	no	28.01
E-MTAB-6386	no	5.71
E-ANND-3	no	4.93

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

5 targeting PGBD4, 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-511-3P	99.99	68.85	1467
HSA-MIR-6818-3P	98.56	68.23	1307
HSA-MIR-432-5P	98.00	68.13	989
HSA-MIR-4653-3P	96.26	67.03	725
HSA-MIR-576-3P	96.14	65.63	773

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

PiggyBac transposable element-derived protein 4 — Q96DM1 (reviewed: Q96DM1)

All UniProt accessions (1): Q96DM1

RefSeq proteins (1): NP_689808* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029526	PGBD	Domain
IPR032718	PGBD4_Znf_C	Domain

Pfam: PF13842, PF13843

UniProt features (9 total): sequence conflict 4, compositionally biased region 3, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96DM1-F1	83.31	0.56

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 35 (showing top): chr15q14, PAX6_01, SHEPARD_CRASH_AND_BURN_MUTANT_DN, DYRK1A_TARGET_GENES, ELF2_TARGET_GENES, KAT5_TARGET_GENES, LHX9_TARGET_GENES, NKX2_3_TARGET_GENES, SALL4_TARGET_GENES, THRA_TARGET_GENES, ZBTB18_TARGET_GENES, ZNF618_TARGET_GENES, MIR432_5P, MIR4653_3P, SETD1A_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

2979 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PGBD4	ERCC6	Q03468	451
PGBD4	TTC9C	Q8N5M4	440
PGBD4	TIGD4	Q8IY51	432
PGBD4	TIGD1	Q96MW7	430
PGBD4	IER5L	Q5T953	402
PGBD4	RMDN1	Q96DB5	399
PGBD4	SPATA2L	Q8IUW3	380
PGBD4	PCBD2	Q9H0N5	356
PGBD4	GIN1	Q9NXP7	356
PGBD4	EXD1	Q8NHP7	351
PGBD4	CD3E	P07766	342
PGBD4	UAP1L1	Q3KQV9	338
PGBD4	ABHD8	Q96I13	335
PGBD4	RUSC2	Q8N2Y8	328
PGBD4	SLC37A2	Q8TED4	325

IntAct

2 interactions, top by confidence:

A	B	Type	Score
PGBD4	PLEC	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (2): PGBD4 (Proximity Label-MS), PGBD4 (Affinity Capture-MS)

ESM2 similar proteins: A4IFA3, A4Z943, A4Z944, A4Z945, B2RRL2, D3Z4R1, F1NQJ3, O43422, O60108, O60290, O96006, P08770, P0CF97, P12258, P16320, P34601, Q09772, Q0VBL1, Q17RP2, Q3EBC8, Q3YK19, Q49AG3, Q4R6P1, Q4W5G0, Q5SVZ6, Q5SXJ3, Q6EKJ0, Q6NT04, Q6R2W3, Q7L775, Q7M3K2, Q86UP8, Q8BUZ3, Q8IY51, Q8IZ13, Q8TBB0, Q8TCP9, Q8TDG4, Q8VEH5, Q95M72

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	63
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

93 predictions. Top by Δscore:

Variant	Effect	Δscore
15:34104200:A:T	donor_gain	0.9900
15:34104187:C:T	donor_gain	0.9400
15:34104231:A:AG	donor_gain	0.9400
15:34104182:G:GT	donor_gain	0.9100
15:34104199:G:GT	donor_gain	0.8700
15:34104227:T:G	donor_gain	0.8500
15:34104190:G:GT	donor_gain	0.8400
15:34102242:GAC:G	donor_gain	0.8200
15:34102242:G:GT	donor_gain	0.7200
15:34102161:G:GT	donor_gain	0.6900
15:34104211:C:G	donor_gain	0.6800
15:34104229:TG:T	donor_gain	0.6800
15:34104225:A:T	donor_gain	0.6600
15:34102244:C:G	donor_gain	0.6500
15:34104425:A:AG	donor_gain	0.6300
15:34104093:G:GT	donor_gain	0.6200
15:34102205:G:GT	donor_gain	0.6000
15:34104230:G:GT	donor_gain	0.5300
15:34102255:A:T	donor_gain	0.5200
15:34104426:A:G	donor_gain	0.5100
15:34104232:T:G	donor_gain	0.4800
15:34104194:A:G	donor_gain	0.4700
15:34104395:G:GT	donor_gain	0.4700
15:34102245:G:GG	donor_gain	0.4500
15:34104230:G:A	donor_gain	0.4500
15:34102247:ATG:A	donor_gain	0.4400
15:34104419:AT:A	donor_gain	0.4400
15:34102161:G:T	donor_gain	0.4100
15:34104239:C:G	donor_gain	0.4100
15:34103342:G:GG	donor_gain	0.4000

AlphaMissense

3877 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:34104257:T:C	F576L	0.997
15:34104259:T:A	F576L	0.997
15:34104259:T:G	F576L	0.997
15:34104101:T:C	F524L	0.994
15:34104103:C:A	F524L	0.994
15:34104103:C:G	F524L	0.994
15:34104254:T:C	C575R	0.992
15:34104218:T:C	C563R	0.991
15:34104254:T:A	C575S	0.991
15:34104255:G:C	C575S	0.991
15:34104227:T:A	C566S	0.990
15:34104228:G:C	C566S	0.990
15:34104269:C:G	H580D	0.990
15:34104218:T:A	C563S	0.989
15:34104219:G:C	C563S	0.989
15:34104271:C:A	H580Q	0.989
15:34104271:C:G	H580Q	0.989
15:34104152:T:A	C541S	0.988
15:34104153:G:C	C541S	0.988
15:34104242:T:C	C571R	0.988
15:34104240:T:C	L570P	0.987
15:34104242:T:A	C571S	0.987
15:34104243:G:C	C571S	0.987
15:34103120:T:C	F197L	0.986
15:34103122:T:A	F197L	0.986
15:34103122:T:G	F197L	0.986
15:34104266:T:G	Y579D	0.986
15:34103984:T:C	F485L	0.985
15:34103986:C:A	F485L	0.985
15:34103986:C:G	F485L	0.985

dbSNP variants (sampled 300 via entrez): RS1000094876 (15:34107944 G>A), RS1000163247 (15:34109183 G>A,C,T), RS1000388264 (15:34106665 A>G), RS1000421144 (15:34106301 G>A,C), RS1000833630 (15:34106151 G>A), RS1001094936 (15:34106409 C>G), RS1001325299 (15:34100517 C>T), RS1001641932 (15:34107516 ATCT>A), RS1002062519 (15:34105146 T>A), RS1002095010 (15:34104875 C>T), RS1002392818 (15:34105751 A>C), RS1002653094 (15:34106029 C>T), RS1002726343 (15:34101414 C>T), RS1002751173 (15:34101103 T>G), RS1004062033 (15:34104525 C>A)

Disease associations

OMIM: gene MIM:621245 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST010725_22	Malaria	3.000000e-06
GCST010725_37	Malaria	3.000000e-06
GCST010725_54	Malaria	5.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
triphenyl phosphate	affects expression	1
avobenzone	decreases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
2,3,5-trichloro-6-phenyl-(1,4)benzoquinone	increases expression	1
Sunitinib	decreases expression	1
Dimethyl Sulfoxide	affects expression	1
Potassium Chloride	decreases expression, decreases response to substance	1
Dronabinol	decreases expression, decreases response to substance	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
Cyclosporine	decreases expression	1
Antirheumatic Agents	decreases expression	1
Okadaic Acid	decreases expression	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

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