PGBD1

piggyBac transposable element derived 1, the group of DNA transposon derived genes|Scavenger receptor cysteine rich domain containing

Basic information

Region (hg38): 6:28281572-28302549

Links

ENSG00000137338 ∙ NCBI:84547 ∙ ∙ HGNC:19398 ∙ Uniprot:Q96JS3 ∙ 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 PGBD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGBD1 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					1	1
missense			33	3	1	37
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	3	2

Variants in PGBD1

This is a list of pathogenic ClinVar variants found in the PGBD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-28283818-A-G		not specified	Uncertain significance (Feb 27, 2024)
6-28283916-G-A		not specified	Likely benign (Jun 29, 2023)
6-28283943-C-T		not specified	Uncertain significance (Apr 19, 2024)
6-28284144-A-T		not specified	Uncertain significance (Aug 22, 2023)
6-28284145-G-T		not specified	Uncertain significance (Dec 07, 2023)
6-28285660-A-G		not specified	Uncertain significance (Jan 26, 2023)
6-28287103-C-T		not specified	Uncertain significance (Aug 30, 2022)
6-28287113-A-G		not specified	Uncertain significance (Mar 13, 2023)
6-28296817-C-G		not specified	Uncertain significance (May 30, 2023)
6-28296852-G-A		not specified	Uncertain significance (Aug 02, 2021)
6-28296900-T-C		not specified	Uncertain significance (Dec 03, 2021)
6-28297899-A-C		not specified	Uncertain significance (Jun 10, 2024)
6-28297907-T-A		not specified	Uncertain significance (Jun 16, 2023)
6-28297909-A-G		not specified	Uncertain significance (Mar 30, 2024)
6-28297921-T-G		not specified	Uncertain significance (Aug 25, 2021)
6-28300735-C-T		not specified	Likely benign (Aug 02, 2021)
6-28300743-C-T		not specified	Uncertain significance (Jun 06, 2023)
6-28300753-C-T		not specified	Uncertain significance (Feb 05, 2024)
6-28300756-C-T		not specified	Uncertain significance (May 18, 2023)
6-28300801-A-G		not specified	Uncertain significance (Apr 06, 2022)
6-28300890-G-A			Benign (Dec 13, 2017)
6-28300906-G-T		not specified	Uncertain significance (Mar 29, 2023)
6-28300980-G-A		not specified	Uncertain significance (Sep 22, 2022)
6-28301067-C-G		not specified	Uncertain significance (Feb 06, 2023)
6-28301097-G-A		not specified	Uncertain significance (Jun 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGBD1	protein_coding	protein_coding	ENST00000405948	6	21013

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.73e-10	0.946	125584	0	164	125748	0.000652

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.857	368	417	0.882	0.0000209	5359
Missense in Polyphen		117	132.58	0.88251		1811
Synonymous	1.33	131	152	0.863	0.00000761	1497
Loss of Function	2.03	20	32.5	0.616	0.00000172	415

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00102	0.00102
Ashkenazi Jewish	0.00199	0.00199
East Asian	0.000381	0.000381
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000884	0.000879
Middle Eastern	0.000381	0.000381
South Asian	0.000261	0.000261
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.968
• rvis_EVS: 1.14
• rvis_percentile_EVS: 92.33

Haploinsufficiency Scores

• pHI: 0.0304
• hipred: N
• hipred_score: 0.158
• ghis: 0.473

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.654

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pgbd1

Gene ontology

• Biological process: regulation of transcription, DNA-templated;receptor-mediated endocytosis
• Cellular component: membrane
• Molecular function: DNA-binding transcription factor activity;scavenger receptor activity;protein binding;identical protein binding