SEC13
SEC13 homolog, nuclear pore and COPII coat complex component, the group of GATOR2 subcomplex|WD repeat domain containing|Nucleoporins|COPII coat complex
Basic information
Region (hg38): 3:10293131-10321112
Previous symbols: [ "D3S1231E", "SEC13L1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (59 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC13 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000183352.3. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 58 | 59 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 58 | 2 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SEC13 | protein_coding | protein_coding | ENST00000350697 | 9 | 28048 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0179 | 0.981 | 125735 | 0 | 13 | 125748 | 0.0000517 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.621 | 172 | 196 | 0.875 | 0.0000112 | 2116 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000904 | 0.0000904 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000704 | 0.0000703 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000673 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
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}.;
- Pathway
- 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;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;MHC class II antigen presentation;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;Immune System;Adaptive Immune System;RHO GTPases Activate Formins;Class I MHC mediated antigen processing & presentation;RHO GTPase Effectors;Signaling by Rho GTPases;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport;Antigen Presentation: Folding, assembly and peptide loading of class I MHC;Cell Cycle, Mitotic
(Consensus)
Recessive Scores
- pRec
- 0.177
Intolerance Scores
- loftool
- 0.493
- rvis_EVS
- -0.43
- rvis_percentile_EVS
- 25.37
Haploinsufficiency Scores
- pHI
- 0.310
- hipred
- Y
- hipred_score
- 0.714
- ghis
- 0.605
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.745
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sec13
- Phenotype
Zebrafish Information Network
- Gene name
- sec13
- Affected structure
- retinal ganglion cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- 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;COPII vesicle coating;mRNA transport;COPII-coated vesicle cargo loading;COPII-coated vesicle budding
- Cellular component
- Golgi membrane;kinetochore;nuclear envelope;nucleoplasm;lysosomal membrane;endoplasmic reticulum membrane;cytosol;ER to Golgi transport vesicle membrane;COPII vesicle coat;nuclear pore outer ring;intracellular membrane-bounded organelle;GATOR2 complex;extracellular exosome
- Molecular function
- protein binding;identical protein binding