PGBD5

piggyBac transposable element derived 5, the group of DNA transposon derived genes

Basic information

Region (hg38): 1:230314489-230426332

Links

ENSG00000177614 ∙ NCBI:79605 ∙ OMIM:616791 ∙ HGNC:19405 ∙ Uniprot:Q8N414 ∙ 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 PGBD5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGBD5 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				2	2	4
missense					2	2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	2	4

Variants in PGBD5

This is a list of pathogenic ClinVar variants found in the PGBD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-230323434-C-T			Benign (May 18, 2018)
1-230325360-C-T			Likely benign (May 18, 2018)
1-230333013-C-T			Likely benign (Jun 01, 2022)
1-230337208-C-T			Benign (May 18, 2018)
1-230357055-C-T			Benign (Aug 05, 2018)
1-230357189-C-T			Benign (Aug 05, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGBD5	protein_coding	protein_coding	ENST00000525115	7	104084

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00212	0.994	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.35	225	290	0.776	0.0000190	2999
Missense in Polyphen		67	101.41	0.66071		1114
Synonymous	-0.550	136	128	1.06	0.00000950	874
Loss of Function	2.54	8	20.4	0.393	0.00000109	220

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000906	0.0000906
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transposase that mediates sequence-specific genomic rearrangements (PubMed:26406119, PubMed:28504702). Can induce genomic rearrangements that inactivate the HPRT1 gene (PubMed:27491780). {ECO:0000269|PubMed:26406119, ECO:0000269|PubMed:27491780, ECO:0000269|PubMed:28504702}.
• Disease: DISEASE: Note=Induces site-specific DNA rearrangements, including intrachromosomal deletions, as well as inversions, duplications and translocations, in rhabdoid tumors that share developmental origin with cells that normally express PGBD5, even though these tumors may not exhibit apparent widespread genomic instability. This activity recurrently targets regulatory elements and tumor suppressor genes and promotes cell transformation. {ECO:0000269|PubMed:28504702}.
• Pathway: Pathways in clear cell renal cell carcinoma (Consensus)

Haploinsufficiency Scores

• pHI: 0.274
• hipred: Y
• hipred_score: 0.663
• ghis: 0.579

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.186

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pgbd5

Gene ontology

• Biological process: nucleic acid phosphodiester bond hydrolysis;non-replicative transposition, DNA-mediated
• Cellular component: nucleus
• Molecular function: endonuclease activity;transposase activity