PGBD4

piggyBac transposable element derived 4, the group of DNA transposon derived genes

Basic information

Region (hg38): 15:34102083-34108686

Links

ENSG00000182405 ∙ NCBI:161779 ∙ ∙ HGNC:19401 ∙ Uniprot:Q96DM1 ∙ 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 PGBD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGBD4 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			33			33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	0	0

Variants in PGBD4

This is a list of pathogenic ClinVar variants found in the PGBD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-34102535-T-A		not specified	Uncertain significance (Jul 09, 2021)
15-34102559-C-T		not specified	Uncertain significance (Mar 14, 2023)
15-34102676-G-A		not specified	Uncertain significance (Mar 19, 2024)
15-34102677-A-G		not specified	Uncertain significance (Aug 04, 2021)
15-34102677-A-T		not specified	Uncertain significance (Nov 25, 2024)
15-34102767-C-T		not specified	Uncertain significance (Feb 26, 2025)
15-34103071-G-T		not specified	Uncertain significance (May 03, 2023)
15-34103082-A-G		not specified	Uncertain significance (Feb 06, 2023)
15-34103121-T-A		not specified	Uncertain significance (Aug 28, 2024)
15-34103208-T-G		not specified	Uncertain significance (Dec 12, 2024)
15-34103423-G-A		not specified	Uncertain significance (Oct 09, 2024)
15-34103463-C-T		not specified	Uncertain significance (Aug 07, 2024)
15-34103522-G-C		not specified	Uncertain significance (Jan 23, 2024)
15-34103544-T-C		not specified	Uncertain significance (Feb 19, 2025)
15-34103655-T-C		not specified	Uncertain significance (Nov 10, 2024)
15-34103688-A-G		not specified	Uncertain significance (Mar 07, 2024)
15-34103691-G-T		not specified	Uncertain significance (Apr 19, 2023)
15-34103699-G-A		not specified	Uncertain significance (Sep 01, 2021)
15-34103732-A-G		not specified	Uncertain significance (Feb 26, 2024)
15-34103800-T-G		not specified	Uncertain significance (Mar 30, 2024)
15-34103844-T-A		not specified	Uncertain significance (Mar 14, 2025)
15-34103862-A-G		not specified	Uncertain significance (Nov 17, 2023)
15-34103864-C-T		not specified	Uncertain significance (Mar 14, 2023)
15-34103871-G-C		not specified	Uncertain significance (Nov 20, 2024)
15-34103886-A-G		not specified	Uncertain significance (Mar 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGBD4	protein_coding	protein_coding	ENST00000397766	1	2318

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.337	0.497	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.49	259	336	0.772	0.0000191	3863
Missense in Polyphen		79	85.273	0.92643		1011
Synonymous	1.61	109	133	0.822	0.00000817	1140
Loss of Function	0.663	0	0.512	0.00	2.15e-8	9

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.889
• rvis_EVS: -0.31
• rvis_percentile_EVS: 31.93

Haploinsufficiency Scores

• pHI: 0.0438
• hipred: N
• hipred_score: 0.238
• ghis: 0.592

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.327

Gene Damage Prediction

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