PGBD4

Chr 15

piggyBac transposable element derived 4

NCBI Gene: 161779 ENSG00000182405 UniProt: Q96DM1 OMIM: 621245

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. [provided by RefSeq, Jul 2008]

OMIM Research

OMIM ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.83

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.83LOEUF

pLI 0.337

Z-score 0.66

OE 0.00 (0.00–1.83)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

1.49Z-score

OE missense 0.77 (0.70–0.85)

259 obs / 335.6 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.00 (0.00–1.83)

0≤0.351.4

Missense OE?0.77 (0.70–0.85)

0≤0.61.4

Synonymous OE?0.82

0≤1.21.6

LoF obs/exp: 0 / 0.5Missense obs/exp: 259 / 335.6Syn Z: 1.61

Background carrier burden — how many people carry a rare variant somewhere in PGBD4?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 120

666 rare PASS variants

Rare truncating (LoF)

1 in 1,000

102 rare PASS variants

Rare synonymous (reference)

1 in 420

267 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for PGBD4. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 150	1 in 1,400
South Asian	~43k	1 in 100	1 in 470
Remaining (unassigned)	~30k	1 in 120	1 in 340
European (Finnish)	~27k	1 in 1,300	1 in 4,400
Admixed American	~22k	1 in 140	1 in 300
African / African American	~21k	1 in 92	1 in 1,600
East Asian	~20k	1 in 120	1 in 2,500
Ashkenazi Jewish	~13k	1 in 450	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 180	≈ 1 in 2,900

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 1 coding exons well covered in gnomAD exomes and genomes.? see exons ↓