SYNJ1

Chr 21

synaptojanin 1

Also known as: DEE53, EIEE53, INPP5G, PARK20

NCBI Gene: 8867ENSG00000159082UniProt: O43426

This gene encodes a phosphoinositide phosphatase that regulates levels of membrane phosphatidylinositol-4,5-bisphosphate. As such, expression of this enzyme may affect synaptic transmission and membrane trafficking. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtParkinson disease 20, early-onset
UniProtDevelopmental and epileptic encephalopathy 53

Clinical highlights

Gene-disease validity (ClinGen)
genetic developmental and epileptic encephalopathy · ARDefinitivesufficient evidence for diagnostic panels
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.
0
Active trials
24
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.33
LOEUF· LoF intol.
—
Mechanism
📖
GeneReview available — SYNJ1
Authoritative clinical overview · Recommended first read
Open GeneReview ↗
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?
0.33LOEUF
pLI 0.427
Z-score 6.61
OE 0.22 (0.16–0.33)
Highly constrained

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

Missense Constraint?
2.25Z-score
OE missense 0.78 (0.73–0.83)
667 obs / 851.7 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?
LoF OE?0.22 (0.16–0.33)
0≤0.351.4
Missense OE?0.78 (0.73–0.83)
0≤0.61.4
Synonymous OE?0.97
0≤1.21.6
LoF obs/exp: 19 / 84.5Missense obs/exp: 667 / 851.7Syn Z: 0.41

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

SYNJ1 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

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