PGBD2

piggyBac transposable element derived 2, the group of DNA transposon derived genes

Basic information

Region (hg38): 1:248906196-248919946

Links

ENSG00000185220 ∙ ∙ ∙ HGNC:19399 ∙ Uniprot:Q6P3X8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PGBD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGBD2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			39			39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	40	0	0

Variants in PGBD2

This is a list of pathogenic ClinVar variants found in the PGBD2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-248913878-A-G		not specified	Uncertain significance (May 27, 2022)
1-248916610-T-C		not specified	Uncertain significance (Nov 17, 2022)
1-248916636-G-A		not specified	Uncertain significance (Apr 26, 2023)
1-248916714-A-G		not specified	Uncertain significance (Nov 01, 2022)
1-248916736-C-T		not specified	Uncertain significance (Sep 16, 2021)
1-248916775-G-T		not specified	Uncertain significance (Oct 29, 2021)
1-248916826-G-A		not specified	Uncertain significance (Nov 15, 2021)
1-248916832-A-G		not specified	Uncertain significance (Apr 20, 2023)
1-248916854-T-A		not specified	Uncertain significance (Sep 01, 2021)
1-248916937-G-A		not specified	Uncertain significance (Feb 12, 2024)
1-248916976-T-C		not specified	Uncertain significance (Aug 03, 2022)
1-248917014-C-G		not specified	Uncertain significance (Dec 19, 2022)
1-248917033-A-G		not specified	Uncertain significance (Nov 12, 2021)
1-248917034-T-G		not specified	Uncertain significance (Dec 07, 2021)
1-248917071-C-T		not specified	Uncertain significance (Aug 09, 2021)
1-248917096-A-G		not specified	Uncertain significance (Dec 13, 2023)
1-248917125-T-G		not specified	Uncertain significance (May 24, 2024)
1-248917212-C-T		not specified	Uncertain significance (Sep 29, 2023)
1-248917269-C-A		not specified	Uncertain significance (May 26, 2024)
1-248917281-A-G		not specified	Uncertain significance (Dec 21, 2022)
1-248917287-G-A		not specified	Uncertain significance (Dec 28, 2022)
1-248917297-C-G		not specified	Uncertain significance (Jun 01, 2023)
1-248917311-G-T		not specified	Uncertain significance (Aug 30, 2021)
1-248917317-G-C		not specified	Uncertain significance (Dec 14, 2023)
1-248917348-A-G		not specified	Uncertain significance (Feb 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGBD2	protein_coding	protein_coding	ENST00000329291	2	13751

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.44e-16	0.00405	125679	0	69	125748	0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.229	349	337	1.04	0.0000190	3934
Missense in Polyphen		82	75.521	1.0858		984
Synonymous	-0.149	129	127	1.02	0.00000695	1135
Loss of Function	-0.467	22	19.8	1.11	0.00000127	226

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000482	0.000481
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000325	0.000299
Middle Eastern	0.000272	0.000272
South Asian	0.000490	0.000490
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.629
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.88

Haploinsufficiency Scores

• pHI: 0.158
• hipred: N
• hipred_score: 0.168
• ghis: 0.642

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.414

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium