SEC24A
protein-codingSEC24 homolog A, COPII coat complex component, the group of COPII coat complex
Gene summary
The protein encoded by this gene belongs to a family of proteins that are homologous to yeast Sec24. This protein is a component of coat protein II (COPII)-coated vesicles that mediate protein transport from the endoplasmic reticulum. COPII acts in the cytoplasm to promote the transport of secretory, plasma membrane, and vacuolar proteins from the endoplasmic reticulum to the golgi complex. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~79.1 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 SEC24A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_021982.3. 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 | 2 | 3 | |||
| missense | 152 | 1 | 153 | |||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 6 | 6 | ||||
| Total | 0 | 0 | 161 | 3 | 0 | 164 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_068817.1 | 23 | MANE Select | |
| Ensembl | ENSP00000381823.2 | 23 | MANE Select | |
| RefSeq | NP_001239160.1 | 13 | Standard | |
| Ensembl | ENSP00000321749.4 | 13 | Standard |
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
- miR-targeted genes in leukocytes - TarBase
- miR-targeted genes in lymphocytes - TarBase
- miR-targeted genes in muscle cell - TarBase
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
- cholesterol homeostasis
Molecular Function
- 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
- ENST00000398844
- Coding exons
- 23
- Length
- 79035
- Individuals with no LoFs
- 124743
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 54
- Defined
- 124797
- p
- 0.000216
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.406 | 551 | 578 | 0.953 | 0.0000288 | 7047 |
| Missense (PolyPhen) | 118 | 141.85 | 0.83185 | 1666 | ||
| Synonymous | -0.557 | 222 | 212 | 1.05 | 0.0000108 | 2230 |
| Loss of Function | 4.12 | 24 | 57.8 | 0.415 | 0.00000302 | 688 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00019 | rare |
| Latino/Admixed American | 0.00016 | 0.00014 | rare |
| Ashkenazi Jewish | 0.00030 | 0.00030 | rare |
| East Asian | 0.00028 | 0.00028 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00024 | 0.00023 | rare |
| South Asian | 0.00032 | 0.00029 | rare |
| Other | 0 | 0.0 | absent |
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:20427317, PubMed:17499046, PubMed:18843296). Plays a central role in cargo selection within the COPII complex and together with SEC24B may have a different specificity compared to SEC24C and SEC24D. May package preferentially cargos with cytoplasmic DxE or LxxLE motifs and may also recognize conformational epitopes (PubMed:17499046, PubMed:18843296). {ECO:0000269|PubMed:17499046, ECO:0000269|PubMed:18843296, ECO:0000269|PubMed:20427317}.;
Recessive Scores
- pRec
- 0.0997
Intolerance Scores
- LoFtool
- 0.355
- RVIS EVS
- -1.06
- RVIS percentile EVS
- 7.55
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.814
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |