SEC16A
protein-codingSEC16 homolog A, endoplasmic reticulum export factor
Gene summary
This gene encodes a protein that forms part of the Sec16 complex. This protein has a role in protein transport from the endoplasmic reticulum (ER) to the Golgi and mediates COPII vesicle formation at the transitional ER. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Feb 2013]
- KIAA0310
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~43.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SEC16A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014866.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 13 | 6 | 22 | ||
| missense | 377 | 35 | 7 | 419 | ||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 386 | 48 | 13 | 447 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055681.1 | 30 | MANE Select | |
| Ensembl | ENSP00000508822.1 | 30 | MANE Select | |
| RefSeq | NP_001263347.1 | 28 | Standard | |
| RefSeq | NP_001424932.1 | 30 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Vesicle-mediated transport
- Membrane Trafficking
- Post-translational protein modification
- Metabolism of proteins
- Transport to the Golgi and subsequent modification
Biological Process
- endoplasmic reticulum to Golgi vesicle-mediated transport
- endoplasmic reticulum organization
- Golgi organization
- substantia nigra development
- protein exit from endoplasmic reticulum
Molecular Function
- protein binding
Cellular Component
- Golgi membrane
- endoplasmic reticulum
- endoplasmic reticulum membrane
- Golgi apparatus
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000313050
- Coding exons
- 30
- Length
- 37593
- Individuals with no LoFs
- 124574
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 75
- Defined
- 124649
- p
- 0.000301
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.472 | 1458 | 1.41e+3 | 1.04 | 0.0000872 | 15157 |
| Missense (PolyPhen) | 434 | 473.1 | 0.91736 | 5336 | ||
| Synonymous | -3.06 | 701 | 605 | 1.16 | 0.0000448 | 4899 |
| Loss of Function | 7.06 | 22 | 97.0 | 0.227 | 0.00000479 | 1110 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00048 | 0.00045 | rare |
| Latino/Admixed American | 0.00050 | 0.00049 | rare |
| Ashkenazi Jewish | 0.00042 | 0.00040 | rare |
| East Asian | 0.00034 | 0.00033 | rare |
| Finnish | 0.00029 | 0.00028 | rare |
| European (Non-Finnish) | 0.00026 | 0.00026 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Defines endoplasmic reticulum exit sites (ERES) and is required for secretory cargo traffic from the endoplasmic reticulum to the Golgi apparatus. SAR1A-GTP-dependent assembly of SEC16A on the ER membrane forms an organized scaffold defining an ERES. Required for normal transitional endoplasmic reticulum (tER) organization. {ECO:0000269|PubMed:17005010, ECO:0000269|PubMed:17192411}.;
Recessive Scores
- pRec
- 0.126
Intolerance Scores
- LoFtool
- 0.999
- RVIS EVS
- -2.29
- RVIS percentile EVS
- 1.23
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.743
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |