PGBD5

Chr 1AR

piggyBac transposable element derived 5

Also known as: NEDSHS

NCBI Gene: 79605ENSG00000177614UniProt: Q8N414OMIM: 616791

PGBD5 encodes a transposase that mediates sequence-specific genomic rearrangements and can induce gene inactivation. Biallelic mutations cause autosomal recessive neurodevelopmental disorder with seizures, hypotonia, and variable spasticity. The gene shows low constraint to loss-of-function variation (pLI 0.002, LOEUF 0.708), consistent with its recessive inheritance pattern.

OMIMResearchSummary from RefSeq, OMIM, UniProt
ARLOEUF 0.711 OMIM phenotype
Clinical Summary— PGBD5
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
44 unique Pathogenic / Likely Pathogenic· 6 VUS of 64 total submissions
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.71LOEUF
pLI 0.002
Z-score 2.54
OE 0.39 (0.23–0.71)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
1.35Z-score
OE missense 0.78 (0.70–0.87)
225 obs / 289.8 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.39 (0.23–0.71)
0≤0.351.4
Missense OE0.78 (0.70–0.87)
0≤0.61.4
Synonymous OE1.06
0≤1.21.6
LoF obs/exp: 8 / 20.4Missense obs/exp: 225 / 289.8Syn Z: -0.55

ClinVar Variant Classifications

64 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic42
Likely Pathogenic2
VUS6
Likely Benign2
Benign4
42
Pathogenic
2
Likely Pathogenic
6
VUS
2
Likely Benign
4
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
4
0
38
0
42
Likely Pathogenic
0
0
2
0
2
VUS
0
0
6
0
6
Likely Benign
0
0
0
2
2
Benign
0
2
0
2
4
Total4246456

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

PGBD5 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients