SEC24C
protein-codingSEC24 homolog C, COPII coat complex component, the group of COPII coat complex
Gene summary
The protein encoded by this gene is a member of the SEC24 subfamily of the SEC23/SEC24 family, which is involved in vesicle trafficking. The encoded protein has similarity to yeast Sec24p component of COPII. COPII is the coat protein complex responsible for vesicle budding from the ER. The product of this gene may play a role in shaping the vesicle, as well as in cargo selection and concentration. Alternatively spliced transcript variants encoding the same protein have been identified. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~27.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0018923
Submitter: Orphanet
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SEC24C variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_198597.3. 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 | 7 | 1 | 9 | ||
| missense | 150 | 4 | 1 | 155 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | 2 | |||
| splice donor/acceptor (+/-2bp) | 8 | 8 | ||||
| Total | 0 | 1 | 161 | 11 | 2 | 175 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_940999.1 | 22 | MANE Select | |
| Ensembl | ENSP00000321845.6 | 22 | MANE Select | |
| RefSeq | NP_004913.2 | 22 | Standard | |
| Ensembl | ENSP00000343405.2 | 22 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| sec24c | Danio rerio | Structure: whole organism Quality: decreased length abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Protein processing in endoplasmic reticulum - Homo sapiens (human)
- Sterol Regulatory Element-Binding Proteins (SREBP) signalling
- Vesicle-mediated transport
- Membrane Trafficking
- Post-translational protein modification
Biological Process
- antigen processing and presentation of peptide antigen via MHC class I
- intracellular protein transport
- endoplasmic reticulum to Golgi vesicle-mediated transport
- antigen processing and presentation of exogenous peptide antigen via MHC class II
- COPII vesicle coating
Molecular Function
- SNARE binding
- protein binding
- zinc ion binding
Cellular Component
- Golgi membrane
- endoplasmic reticulum membrane
- cytosol
- ER to Golgi transport vesicle membrane
- COPII vesicle coat
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000339365
- Coding exons
- 22
- Length
- 27800
- Individuals with no LoFs
- 125738
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 10
- Defined
- 125748
- p
- 0.0000398
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.50 | 517 | 622 | 0.831 | 0.0000346 | 7029 |
| Missense (PolyPhen) | 180 | 265.59 | 0.67773 | 3076 | ||
| Synonymous | -0.529 | 251 | 241 | 1.04 | 0.0000127 | 2294 |
| Loss of Function | 6.21 | 4 | 52.6 | 0.0760 | 0.00000269 | 595 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000062 | 0.000062 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). The coat has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules for their transport to the Golgi complex (PubMed:10214955, PubMed:17499046, PubMed:18843296, PubMed:20427317). Plays a central role in cargo selection within the COPII complex and together with SEC24D may have a different specificity compared to SEC24A and SEC24B (PubMed:17499046, PubMed:20427317, PubMed:18843296). May more specifically package GPI-anchored proteins through the cargo receptor TMED10 (PubMed:20427317). May also be specific for IxM motif-containing cargos like the SNAREs GOSR2 and STX5 (PubMed:18843296). {ECO:0000269|PubMed:10214955, ECO:0000269|PubMed:17499046, ECO:0000269|PubMed:18843296, ECO:0000269|PubMed:20427317}.;
Recessive Scores
- pRec
- 0.0953
Intolerance Scores
- LoFtool
- 0.158
- RVIS EVS
- -0.97
- RVIS percentile EVS
- 8.98
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.866
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |