SEC13
protein-codingSEC13 homolog, nuclear pore and COPII coat complex component, the group of GATOR2 subcomplex|WD repeat domain containing|Nucleoporins|COPII coat complex
Gene summary
The protein encoded by this gene belongs to the SEC13 family of WD-repeat proteins. It is a constituent of the endoplasmic reticulum and the nuclear pore complex. It has similarity to the yeast SEC13 protein, which is required for vesicle biogenesis from endoplasmic reticulum during the transport of proteins. Multiple alternatively spliced transcript variants have been found. [provided by RefSeq, Oct 2008]
- D3S1231E
- SEC13L1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~28.0 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 SEC13 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_183352.3. 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 | 1 | 1 | 2 | |||
| missense | 66 | 1 | 67 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 73 | 2 | 0 | 75 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_899195.1 | 9 | MANE Select | |
| Ensembl | ENSP00000312122.4 | 9 | MANE Select | |
| RefSeq | NP_001129498.1 | 9 | Standard | |
| RefSeq | NP_001129704.1 | 8 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| sec13 | Danio rerio | Structure: retinal ganglion cell Quality: decreased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- mTOR signaling pathway - Homo sapiens (human)
- Protein processing in endoplasmic reticulum - Homo sapiens (human)
- RNA transport - Homo sapiens (human)
- Sterol Regulatory Element-Binding Proteins (SREBP) signalling
- Signal Transduction
Biological Process
- antigen processing and presentation of peptide antigen via MHC class I
- intracellular protein transport
- antigen processing and presentation of exogenous peptide antigen via MHC class II
- positive regulation of TOR signaling
- protein exit from endoplasmic reticulum
Molecular Function
- protein binding
- identical protein binding
Cellular Component
- Golgi membrane
- kinetochore
- nuclear envelope
- nucleoplasm
- lysosomal membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000350697
- Coding exons
- 9
- Length
- 28048
- Individuals with no LoFs
- 125735
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 13
- Defined
- 125748
- p
- 0.0000517
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.621 | 172 | 196 | 0.875 | 0.0000112 | 2116 |
| Missense (PolyPhen) | 49 | 62.875 | 0.77933 | 707 | ||
| Synonymous | 1.18 | 70 | 83.7 | 0.837 | 0.00000569 | 599 |
| Loss of Function | 2.93 | 7 | 21.7 | 0.322 | 0.00000109 | 217 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000070 | 0.000070 | rare |
| South Asian | 0.000067 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Functions as a component of the nuclear pore complex (NPC) and the COPII coat. At the endoplasmic reticulum, SEC13 is involved in the biogenesis of COPII-coated vesicles. {ECO:0000269|PubMed:8972206}.;
Recessive Scores
- pRec
- 0.177
Intolerance Scores
- LoFtool
- 0.493
- RVIS EVS
- -0.43
- RVIS percentile EVS
- 25.37
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.745
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |