PDZRN3

Chr 3

PDZ domain containing ring finger 3

Also known as: LNX3, SEMACAP3, SEMCAP3

This gene encodes a RING-type E3 ubiquitin ligase that regulates muscle-specific kinase (MUSK) levels on muscle cells by mediating its ubiquitination and degradation, contributing to terminal muscle differentiation. Mutations cause autosomal recessive congenital myasthenic syndrome, a neuromuscular junction disorder presenting in infancy or early childhood with muscle weakness, fatigue, and respiratory difficulties. The gene is highly constrained against loss-of-function variants, indicating that complete loss of protein function is likely not tolerated.

OMIMResearchSummary from RefSeq, UniProt
LOFmechanismLOEUF 0.30
Clinical SummaryPDZRN3
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.98). One damaged copy is likely sufficient to cause disease.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

LoF intolerant — likely haploinsufficient
LoF Constraint
0.30LOEUF
pLI 0.985
Z-score 4.68
OE 0.14 (0.070.30)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
-0.01Z-score
OE missense 1.00 (0.941.07)
623 obs / 622.6 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.14 (0.070.30)
00.351.4
Missense OE1.00 (0.941.07)
00.61.4
Synonymous OE1.15
01.21.6
LoF obs/exp: 5 / 34.7Missense obs/exp: 623 / 622.6Syn Z: -2.02
DN
0.4289th %ile
GOF
0.5269th %ile
LOF
0.70top 10%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.30

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

PDZRN3 · 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

No active trials found for this gene.

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Clinical Literature
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