SEC23A
SEC23 homolog A, COPII coat complex component, the group of COPII coat complex
Basic information
Region (hg38): 14:39031919-39109646
Links
Phenotypes
GenCC
Source:
- craniolenticulosutural dysplasia (Limited), mode of inheritance: AR
- craniolenticulosutural dysplasia (Supportive), mode of inheritance: AR
- craniolenticulosutural dysplasia (Limited), mode of inheritance: AR
- craniolenticulosutural dysplasia (Limited), mode of inheritance: Unknown
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Craniolenticulosutural dysplasia | AD/AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Musculoskeletal; Ophthalmologic | 12677423; 16980979; 21039434; 34580982 |
ClinVar
This is a list of variants' phenotypes submitted to
- Craniolenticulosutural_dysplasia (99 variants)
- not_specified (62 variants)
- not_provided (20 variants)
- SEC23A-related_disorder (7 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC23A gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006364.4. 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 | 25 | 26 | ||||
| missense | 102 | 107 | ||||
| nonsense | 5 | |||||
| start loss | 0 | |||||
| frameshift | 3 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 1 | 2 | 110 | 28 | 1 |
Highest pathogenic variant AF is 0.000007436778
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SEC23A | protein_coding | protein_coding | ENST00000307712 | 19 | 77728 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.07e-11 | 0.999 | 125692 | 0 | 56 | 125748 | 0.000223 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.78 | 319 | 422 | 0.756 | 0.0000216 | 5009 |
| Missense in Polyphen | 77 | 124.95 | 0.61626 | 1500 | ||
| Synonymous | 0.507 | 123 | 130 | 0.944 | 0.00000602 | 1476 |
| Loss of Function | 3.01 | 26 | 48.7 | 0.534 | 0.00000270 | 527 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000437 | 0.000437 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.000599 | 0.000598 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000194 | 0.000193 |
| Middle Eastern | 0.000599 | 0.000598 |
| South Asian | 0.000229 | 0.000229 |
| Other | 0.00 | 0.00 |
dbNSFP
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. {ECO:0000269|PubMed:16980979, ECO:0000269|PubMed:17499046, ECO:0000269|PubMed:18843296, ECO:0000269|PubMed:27551091, ECO:0000269|PubMed:8898360}.;
- Disease
- DISEASE: Craniolenticulosutural dysplasia (CLSD) [MIM:607812]: Autosomal recessive syndrome characterized by late-closing fontanels, sutural cataracts, facial dysmorphisms and skeletal defects. {ECO:0000269|PubMed:16980979}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Protein processing in endoplasmic reticulum - Homo sapiens (human);Sterol Regulatory Element-Binding Proteins (SREBP) signalling;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;MHC class II antigen presentation;Immune System;Adaptive Immune System;Class I MHC mediated antigen processing & presentation;Cargo concentration in the ER;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport;Antigen Presentation: Folding, assembly and peptide loading of class I MHC
(Consensus)
Recessive Scores
- pRec
- 0.168
Intolerance Scores
- loftool
- 0.500
- rvis_EVS
- -0.78
- rvis_percentile_EVS
- 12.88
Haploinsufficiency Scores
- pHI
- 0.689
- hipred
- Y
- hipred_score
- 0.589
- ghis
- 0.657
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.970
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sec23a
- Phenotype
- growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- sec23a
- Affected structure
- pharyngeal arch cartilage
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- 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;positive regulation of GTPase activity;COPII vesicle coating;protein localization to plasma membrane;COPII-coated vesicle cargo loading
- Cellular component
- endoplasmic reticulum membrane;cytosol;ER to Golgi transport vesicle membrane;extrinsic component of membrane;COPII vesicle coat;endoplasmic reticulum exit site
- Molecular function
- GTPase activator activity;protein binding;zinc ion binding