PGBD2

Summary

PGBD2 (piggyBac transposable element derived 2, HGNC:19399) is a protein-coding gene on chromosome 1q44, encoding PiggyBac transposable element-derived protein 2 (Q6P3X8).

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. The exact function of this gene is not known. Two transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 267002 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 118 total — 1 pathogenic
• MANE Select transcript: NM_170725

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19399
Approved symbol	PGBD2
Name	piggyBac transposable element derived 2
Location	1q44
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000185220
Ensembl biotype	protein_coding
Entrez	267002

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000329291, ENST00000355360, ENST00000462488, ENST00000935434

RefSeq mRNA: 2 — MANE Select: NM_170725 NM_001017434, NM_170725

CCDS: CCDS31128, CCDS31129

Canonical transcript exons

ENST00000329291 — 3 exons

Exon	Start	End
ENSE00001312561	248916602	248919146
ENSE00001637224	248906235	248906342
ENSE00003610993	248913816	248913879

Expression profiles

Bgee: expression breadth ubiquitous, 223 present calls, max score 80.67.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.5115 / max 54.2742, expressed in 1628 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
9662	4.5027	1626
9663	0.0089	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
granulocyte	CL:0000094	80.67	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.49	gold quality
left testis	UBERON:0004533	79.08	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.07	gold quality
testis	UBERON:0000473	78.39	gold quality
right testis	UBERON:0004534	78.33	gold quality
leukocyte	CL:0000738	78.30	gold quality
monocyte	CL:0000576	78.20	gold quality
oocyte	CL:0000023	77.92	gold quality
mucosa of transverse colon	UBERON:0004991	77.32	gold quality
rectum	UBERON:0001052	76.80	gold quality
spleen	UBERON:0002106	76.73	gold quality
lymph node	UBERON:0000029	76.49	gold quality
body of pancreas	UBERON:0001150	75.94	gold quality
right lobe of liver	UBERON:0001114	75.91	gold quality
myocardium	UBERON:0002349	75.83	silver quality
gingival epithelium	UBERON:0001949	75.80	silver quality
mucosa of sigmoid colon	UBERON:0004993	75.50	gold quality
lower esophagus mucosa	UBERON:0035834	75.34	gold quality
upper arm skin	UBERON:0004263	75.31	silver quality
right lobe of thyroid gland	UBERON:0001119	75.13	gold quality
gingiva	UBERON:0001828	75.13	gold quality
vermiform appendix	UBERON:0001154	74.91	gold quality
pancreas	UBERON:0001264	74.86	gold quality
germinal epithelium of ovary	UBERON:0001304	74.86	silver quality
islet of Langerhans	UBERON:0000006	74.84	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	74.69	silver quality
pancreatic ductal cell	CL:0002079	74.52	silver quality
gall bladder	UBERON:0002110	74.45	gold quality
small intestine Peyer’s patch	UBERON:0003454	74.44	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.91

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

43 targeting PGBD2, 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-3646	100.00	73.56	5283
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-6759-5P	99.99	66.54	785
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-8080	99.82	67.52	1342
HSA-MIR-4517	99.76	69.19	1867
HSA-MIR-4666B	99.64	68.69	1282
HSA-MIR-510-3P	99.54	70.06	2965
HSA-MIR-5004-3P	99.54	68.27	1371
HSA-MIR-6083	99.47	68.73	2393
HSA-MIR-2115-3P	99.31	69.68	2026
HSA-MIR-223-5P	99.24	68.82	1206
HSA-MIR-4687-5P	99.14	66.26	488

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

PiggyBac transposable element-derived protein 2 — Q6P3X8 (reviewed: Q6P3X8)

All UniProt accessions (1): Q6P3X8

Isoforms (2)

UniProt ID	Names	Canonical?
Q6P3X8-1	1	yes
Q6P3X8-2	2

RefSeq proteins (2): NP_001017434, NP_733843* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029526	PGBD	Domain
IPR052638	PiggyBac_TE-derived	Family

Pfam: PF13843

UniProt features (3 total): chain 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6P3X8-F1	83.55	0.60

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 52 (showing top): chr1q44, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, CBX5_TARGET_GENES, ID2_TARGET_GENES, KAT2A_TARGET_GENES, NCOA6_TARGET_GENES, SFMBT1_TARGET_GENES, SNIP1_TARGET_GENES, TOP2B_TARGET_GENES, ZNF2_TARGET_GENES, ZNF274_TARGET_GENES, ZNF391_TARGET_GENES, ZNF407_TARGET_GENES, ZNF524_TARGET_GENES, ZNF592_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA binding	1

Protein interactions and networks

STRING

344 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PGBD2	ZBED8	Q8IZ13	617
PGBD2	THAP9	Q9H5L6	555
PGBD2	POGK	Q9P215	524
PGBD2	PGBD5	Q8N414	513
PGBD2	ZNF862	O60290	510
PGBD2	BET1L	Q9NYM9	481
PGBD2	ERCC6	Q03468	480
PGBD2	ZNF672	Q499Z4	473
PGBD2	NAIF1	Q69YI7	453
PGBD2	ZNF385D	Q9H6B1	447
PGBD2	HARBI1	Q96MB7	445
PGBD2	GNL1	P36915	440
PGBD2	TP53TG3	Q9ULZ0	398
PGBD2	TRPC4AP	Q8TEL6	386
PGBD2	GIN1	Q9NXP7	384

IntAct

9 interactions, top by confidence:

A	B	Type	Score
PGBD1	SCAND1	psi-mi:“MI:0914”(association)	0.940
PGBD1	ZNF24	psi-mi:“MI:0914”(association)	0.900
PGBD1	ZNF213	psi-mi:“MI:0914”(association)	0.530
FAXC	METTL15	psi-mi:“MI:0914”(association)	0.350
FTL	SH3PXD2B	psi-mi:“MI:0914”(association)	0.350
FAXC	POLRMT	psi-mi:“MI:0914”(association)	0.350
FTL		psi-mi:“MI:0914”(association)	0.350

BioGRID (7): PGBD2 (Affinity Capture-MS), PGBD2 (Affinity Capture-MS), PGBD2 (Affinity Capture-MS), PGBD2 (Affinity Capture-MS), PGBD2 (Protein-peptide), TFRC (Cross-Linking-MS (XL-MS)), PGBD2 (Affinity Capture-MS)

ESM2 similar proteins: A0A2P1BRP3, A0A2P1BRQ0, A0ZSK3, A0ZSK4, A4IFA3, A4Z943, A4Z944, A4Z945, B2RD01, B2RRL2, O43422, O60108, O96006, P0CF97, P12258, P34601, P49777, Q09575, Q0VBL1, Q17RP2, Q2T9S8, Q3EBC8, Q49AG3, Q4R6P1, Q4W5G0, Q5SVZ6, Q6EKJ0, Q6NT04, Q6P3X8, Q6R2W3, Q7L775, Q7M3K2, Q7TSV6, Q86UP8, Q8BUZ3, Q8BV66, Q8CBA2, Q8IY51, Q8IZ13, Q8TCP9

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

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	109
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
442386	GRCh37/hg19 1p36.33-q44(chr1:849467-249224684)x3	Pathogenic

SpliceAI

916 predictions. Top by Δscore:

Variant	Effect	Δscore
1:248913813:CAGGT:C	acceptor_loss	1.0000
1:248913814:A:AG	acceptor_gain	1.0000
1:248913814:AGGT:A	acceptor_loss	1.0000
1:248913815:G:GG	acceptor_gain	1.0000
1:248913875:TCCAG:T	donor_loss	1.0000
1:248913876:CCAG:C	donor_loss	1.0000
1:248913877:CAGG:C	donor_loss	1.0000
1:248913878:AGGTA:A	donor_loss	1.0000
1:248913879:GGT:G	donor_loss	1.0000
1:248913880:GT:G	donor_loss	1.0000
1:248913881:T:G	donor_loss	1.0000
1:248913815:GGTT:G	acceptor_gain	0.9900
1:248916601:GAGAT:G	acceptor_gain	0.9900
1:248916999:C:G	donor_gain	0.9900
1:248906490:G:GT	donor_gain	0.9800
1:248906517:G:GT	donor_gain	0.9800
1:248913814:AG:A	acceptor_gain	0.9800
1:248913815:GG:G	acceptor_gain	0.9800
1:248913815:GGTTC:G	acceptor_gain	0.9800
1:248916600:A:AG	acceptor_gain	0.9800
1:248916601:G:GG	acceptor_gain	0.9800
1:248916601:GA:G	acceptor_gain	0.9800
1:248913811:TACAG:T	acceptor_gain	0.9700
1:248914504:G:GT	donor_gain	0.9700
1:248906341:AG:A	donor_loss	0.9600
1:248906342:GGTAG:G	donor_loss	0.9600
1:248906343:G:GC	donor_loss	0.9600
1:248906344:T:A	donor_loss	0.9600
1:248906485:G:GT	donor_gain	0.9600
1:248906491:A:T	donor_gain	0.9600

AlphaMissense

3942 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:248918304:T:A	C574S	0.997
1:248918305:G:C	C574S	0.997
1:248918340:T:C	F586L	0.997
1:248918342:C:A	F586L	0.997
1:248918342:C:G	F586L	0.997
1:248918271:T:A	C563S	0.996
1:248918271:T:C	C563R	0.996
1:248918272:G:C	C563S	0.996
1:248918304:T:C	C574R	0.996
1:248918337:T:C	C585R	0.996
1:248918352:C:G	H590D	0.996
1:248918280:T:A	C566S	0.995
1:248918281:G:C	C566S	0.995
1:248918326:T:A	V581D	0.995
1:248918337:T:A	C585S	0.995
1:248918338:G:C	C585S	0.995
1:248918280:T:C	C566R	0.994
1:248918313:T:A	C577S	0.994
1:248918314:G:C	C577S	0.994
1:248918354:C:A	H590Q	0.994
1:248918354:C:G	H590Q	0.994
1:248917149:A:C	S189R	0.993
1:248917151:T:A	S189R	0.993
1:248917151:T:G	S189R	0.993
1:248918313:T:C	C577R	0.993
1:248917185:T:A	W201R	0.992
1:248917185:T:C	W201R	0.992
1:248918240:C:A	H552Q	0.992
1:248918240:C:G	H552Q	0.992
1:248918305:G:A	C574Y	0.992

dbSNP variants (sampled 300 via entrez): RS1000051404 (1:248872252 A>G), RS1000056410 (1:248899828 A>G), RS1000145049 (1:248915581 C>A,T), RS1000171504 (1:248885828 G>A), RS1000186437 (1:248920341 C>G,T), RS1000291658 (1:248888973 A>G), RS1000300462 (1:248893121 A>G), RS1000323028 (1:248920526 TTTTC>T), RS1000323416 (1:248887714 G>T), RS1000342186 (1:248929515 G>A), RS1000346542 (1:248874757 A>G), RS1000346544 (1:248906922 G>A), RS1000365927 (1:248924696 GACA>G), RS1000506013 (1:248916556 G>C), RS1000519278 (1:248919113 T>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST006462_4	Uterine fibroids	4.000000e-09
GCST009560_3	Decreased low contrast letter acuity in multiple sclerosis	2.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008385	visual acuity measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
triphenyl phosphate	affects expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
sodium arsenite	decreases expression	1
ferrous chloride	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
abrine	decreases expression	1
licochalcone B	increases expression	1
Sunitinib	decreases expression	1
Air Pollutants, Occupational	decreases expression	1
Benzo(a)pyrene	increases expression	1
Ethyl Methanesulfonate	increases expression	1
Methyl Methanesulfonate	increases expression	1
Nickel	decreases expression	1
Niclosamide	decreases expression	1
Rotenone	decreases expression	1
Smoke	decreases expression	1
Thimerosal	increases expression	1
Urethane	increases expression	1
Cyclosporine	decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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