SNAP29

Chr 22

synaptosome associated protein 29

Also known as: CEDNIK, SNAP-29

NCBI Gene: 9342ENSG00000099940UniProt: O95721

This gene, a member of the SNAP25 gene family, encodes a protein involved in multiple membrane trafficking steps. Two other members of this gene family, SNAP23 and SNAP25, encode proteins that bind a syntaxin protein and mediate synaptic vesicle membrane docking and fusion to the plasma membrane. The protein encoded by this gene binds tightly to multiple syntaxins and is localized to intracellular membrane structures rather than to the plasma membrane. While the protein is mostly membrane-bound, a significant fraction of it is found free in the cytoplasm. Use of multiple polyadenylation sites has been noted for this gene. [provided by RefSeq, Jul 2008]

Primary Disease Associations & Inheritance

UniProtCerebral dysgenesis, neuropathy, ichthyosis, and palmoplantar keratoderma syndrome
596
ClinVar variants
283
Pathogenic / LP
0.01
pLI score
0
Active trials
Clinical Summary— SNAP29
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.01) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
283 Pathogenic / Likely Pathogenic· 180 VUS of 596 total submissions
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
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.
0.86LOEUF
pLI 0.014
Z-score 1.91
OE 0.41 (0.21–0.86)
Tolerant

Typical tolerance to LoF variation

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.
-0.87Z-score
OE missense 1.20 (1.06–1.36)
178 obs / 148.1 exp
Tolerant

Tolerant to missense variation

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.0.41 (0.21–0.86)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.20 (1.06–1.36)
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.0.74
0≤1.21.6
LoF obs/exp: 5 / 12.2Missense obs/exp: 178 / 148.1Syn Z: 1.52

ClinVar Variant Classifications

596 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic240
Likely Pathogenic43
VUS180
Likely Benign116
Benign11
Conflicting6
240
Pathogenic
43
Likely Pathogenic
180
VUS
116
Likely Benign
11
Benign
6
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
5
0
235
0
240
Likely Pathogenic
6
2
35
0
43
VUS
0
82
98
0
180
Likely Benign
0
3
47
66
116
Benign
0
0
10
1
11
Conflicting
—6
Total118742567596

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

View in ClinVar →

Protein Context — Lollipop Plot

SNAP29 · protein map & ClinVar variants

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

Gene2Phenotype Curations

SNAP29-related cerebral dysgenesis, neuropathy, ichthyosis, and palmoplantar keratoderma syndrome (CEDNIK syndrome)

strong
ARLoss Of FunctionAbsent Gene Product
Dev. DisordersSkin
G2P ↗

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

OMIM — Genotype-Phenotype

OMIM

No OMIM entries found.

Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Review of the Pathophysiology and Clinical Manifestations of 22q11.2 Deletion and Duplication Syndromes.
Purow J et al.·Clin Rev Allergy Immunol
2025Review
Snapshots from within the cell: Novel trafficking and non trafficking functions of Snap29 during tissue morphogenesis.
Smeele PH et al.·Semin Cell Dev Biol
2023Review
CEDNIK syndrome with phenotypic variability.
Nanda A et al.·Pediatr Dermatol
2022
Saikosaponin D exacerbates acetaminophen-induced liver injury by sabotaging GABARAP-SNARE complex assembly in protective autophagy.
Fan G et al.·Phytomedicine
2025
NK cell-derived GZMB (granzyme B) suppresses glioblastoma radioresistance by blocking SDC1-mediated autophagosome maturation.
Yan J et al.·Autophagy
2026
MiR-7 inhibits progression of glioblastoma by impairing autophagy resolution, energy metabolism and ECM remodeling.
Torrecilla-Parra M et al.·J Exp Clin Cancer Res
2025Functional
A novel autophagy inhibitor berbamine blocks SNARE-mediated autophagosome-lysosome fusion through upregulation of BNIP3.
Fu R et al.·Cell Death Dis
2018
CEDNIK syndrome in a Brazilian patient with compound heterozygous pathogenic variants.
Nunes N et al.·Eur J Med Genet
2022
Genetic Drivers of Kidney Defects in the DiGeorge Syndrome.
Lopez-Rivera E et al.·N Engl J Med
2017
Genotype-phenotype correlations of Berardinelli-Seip congenital lipodystrophy and novel candidate genes prediction.
Ren M et al.·Orphanet J Rare Dis
2020
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Z-Guggulsterone Inhibits Triple-Negative Breast Cancer Progression by Blocking Autophagosome-Lysosome Fusion via OGT-Mediated SNAP29 O-GlcNAcylation.
Qian D et al.·Phytother Res
2026
HRD1 negatively regulates autolysosome formation by inhibiting liquid-liquid phase separation of SNAP29.
Qu W et al.·Cell Rep
2026
METTL3-dependent m6A modification of SNAP29 induces "autophagy-mitochondrial crisis" in the ischemic microenvironment after soft tissue transplantation.
Yang N et al.·Autophagy
2025
Corrigendum to "STING guides the STX17-SNAP29-VAMP8 complex assembly to control autophagy" [Cell Insight 3 (2024) 100147].
Song X et al.·Cell Insight
2025🔓 Open Access
purpleoid 1 , a classic Drosophila eye color mutation, is an allele of the t-SNARE-encoding gene SNAP29.
Dean DM et al.·MicroPubl Biol
2025🔓 Open Access
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