SEC16A: A Key Regulator of ER-to-Golgi Transport and COPII Vesicle Formation
Comprehensive genomic and proteomic analysis of SEC16A, a scaffold protein essential for endoplasmic reticulum exit sites.
Gene Information Card
| Symbol | SEC16A |
|---|---|
| Full Name | SEC16 homolog A, endoplasmic reticulum exit site protein |
| Gene Type | protein-coding |
| Chromosomal Location | 9q34.3 |
| NCBI Gene ID | 9919 ncbi.nlm.nih.gov/gene/9919 |
| Ensembl ID | ENSG00000136826 |
| UniProt ID | O15027 |
| OMIM ID | 612855 |
| HGNC ID | 29006 |
| Aliases | KIAA0310, SEC16L, p250 |
Description
SEC16A encodes a large scaffold protein localized to endoplasmic reticulum (ER) exit sites. It is essential for the formation of COPII-coated vesicles that mediate protein transport from the ER to the Golgi apparatus. SEC16A interacts with multiple COPII components and regulates the size and number of ER exit sites.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Breast cancer | SEC16A overexpression may enhance secretory capacity, promoting tumor growth and metastasis. | COSMIC; PMID: 25691885 |
| Colorectal cancer | SEC16A mutations and copy number alterations observed; potential role in altered protein trafficking. | COSMIC; PMID: 26619011 |
| Neurodevelopmental disorders | Rare SEC16A variants identified in patients with intellectual disability and autism spectrum disorder. | ClinVar; PMID: 28135719 |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Brain | 12.5 | Medium |
| Liver | 8.3 | Low |
| Kidney | 10.1 | Medium |
| Testis | 15.2 | High |
| Pancreas | 6.7 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| HeLa | 14.0 | High expression |
| HEK293 | 11.5 | Medium expression |
| MCF7 | 9.8 | Medium expression |
| HepG2 | 7.2 | Low expression |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.2875C>T (p.Arg959Trp) | Missense | <0.01% | Alters protein stability; reported in ClinVar as uncertain significance |
| c.4420G>A (p.Glu1474Lys) | Missense | <0.01% | Located in conserved region; functional impact unknown |
| c.1234_1235insA | Frameshift | <0.01% | Predicted loss of function; associated with neurodevelopmental phenotype |
Mutation functional classification
Loss of Function (LOF)
Frameshift and nonsense mutations in SEC16A are predicted to cause loss of function, impairing COPII vesicle formation and ER-to-Golgi transport.
Gain of Function (GOF)
No confirmed gain-of-function mutations reported in SEC16A.
Dominant Negative (DN)
Some missense variants may act in a dominant-negative manner by disrupting SEC16A interactions with COPII components, but evidence is limited.
View complete mutation data：
Gene Ontology (GO)
Pathways
• COPII-mediated vesicle transport (REACTOME R-HSA-204005)
• ER to Golgi anterograde transport (REACTOME R-HSA-199977)
• Vesicle-mediated transport (REACTOME R-HSA-5653656)
Protein Summary
SEC16A is a 2355-amino acid scaffold protein that localizes to ER exit sites. It contains multiple coiled-coil domains and a conserved SEC16 domain. SEC16A binds to COPII coat proteins (e.g., SAR1B, SEC23/24, SEC13/31) and is required for the formation of large, functional ER exit sites. It also interacts with other trafficking regulators such as TFG and cTAGE5. SEC16A is ubiquitously expressed with highest levels in testis and brain.
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