STX5

Chr 11AR

syntaxin 5

Also known as: CDG2AA, SED5, STX5A

NCBI Gene: 6811ENSG00000162236UniProt: Q13190

This gene encodes a member of the syntaxin or t-SNARE (target-SNAP receptor) family. These proteins are found on cell membranes and serve as the targets for v-SNAREs (vesicle-SNAP receptors), permitting specific synaptic vesicle docking and fusion. The encoded protein regulates endoplasmic reticulum to Golgi transport and plays a critical role in autophagy. Autoantibodies targeting the encoded protein may be a diagnostic marker for endometriosis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Sep 2011]

Primary Disease Associations & Inheritance

?Congenital disorder of glycosylation, type IIaaMIM #620454
AR
58
ClinVar variants
0
Pathogenic / LP
0.84
pLI score
0
Active trials
Clinical Summary— STX5
⚡
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.84) — some intolerance to loss-of-function variants.
📋
ClinVar Variants
58 total variants — no pathogenic classifications of 58 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.40LOEUF
pLI 0.843
Z-score 3.43
OE 0.16 (0.07–0.40)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.40Z-score
OE missense 0.92 (0.82–1.04)
190 obs / 206.2 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.16 (0.07–0.40)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.92 (0.82–1.04)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.06
0≤1.21.6
LoF obs/exp: 3 / 19.3Missense obs/exp: 190 / 206.2Syn Z: -0.43

ClinVar Variant Classifications

58 submitted variants in ClinVar

ClinVar

Classification Summary

Protein Context — Lollipop Plot

STX5 · protein map & ClinVar variants

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

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
SYNTAXIN 5; STX5
MIM #603189 · *

?Congenital disorder of glycosylation, type IIaa

MIM #620454

Molecular basis of disorder known

Autosomal recessive
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Proteomic profiles of peritoneal fluid-derived small extracellular vesicles correlate with patient outcome in ovarian cancer.
Quiralte M et al.·J Clin Invest
2024Clinical trial
Identification of anti-syntaxin 5 autoantibody as a novel serum marker of endometriosis.
Nabeta M et al.·J Reprod Immunol
2011Clinical trial
Stx5 is a novel interactor of VLDL-R to affect its intracellular trafficking and processing.
Wagner T et al.·Exp Cell Res
2013
Congenital disorder of glycosylation caused by starting site-specific variant in syntaxin-5.
Linders PTA et al.·Nat Commun
2021
Dispatch and delivery at the ER-Golgi interface: how endothelial cells tune their hemostatic response.
Kat M et al.·FEBS J
2022
Study on biomarkers of homocysteine-induced transformation of vascular smooth muscle cells into foam cells.
Wang X et al.·Sci Rep
2026
Identification of biomarkers in common chronic lung diseases by co-expression networks and drug-target interactions analysis.
Maghsoudloo M et al.·Mol Med
2020
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

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