SEC31A
SEC31 homolog A, COPII coat complex component, the group of COPII coat complex|WD repeat domain containing
Basic information
Region (hg38): 4:82818509-82901166
Previous symbols: [ "SEC31L1" ]
Links
Phenotypes
GenCC
Source:
- neurodevelopmental disorder with spastic quadriplegia, optic atrophy, seizures, and structural brain anomalies (Limited), mode of inheritance: AR
- neurodevelopmental disorder with spastic quadriplegia, optic atrophy, seizures, and structural brain anomalies (Limited), mode of inheritance: Unknown
- neurodevelopmental disorder with spastic quadriplegia, optic atrophy, seizures, and structural brain anomalies (Limited), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Halperin-Birk syndrome | 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 | Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic | 30464055 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (109 variants)
- not_provided (20 variants)
- Neurodevelopmental_disorder_with_spastic_quadriplegia,_optic_atrophy,_seizures,_and_structural_brain_anomalies (3 variants)
- SEC31A-related_disorder (3 variants)
- Kaya-Barakat-Masson_syndrome (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC31A gene is commonly pathogenic or not. These statistics are base on transcript: NM_001077207.4. 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 | 9 | |||||
| missense | 112 | 118 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 2 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 1 | 0 | 113 | 12 | 4 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SEC31A | protein_coding | protein_coding | ENST00000395310 | 26 | 82506 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000788 | 1.00 | 125528 | 1 | 218 | 125747 | 0.000871 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.23 | 559 | 647 | 0.864 | 0.0000320 | 7945 |
| Missense in Polyphen | 127 | 177.4 | 0.71591 | 2240 | ||
| Synonymous | -0.614 | 240 | 228 | 1.05 | 0.0000118 | 2390 |
| Loss of Function | 5.35 | 21 | 68.9 | 0.305 | 0.00000363 | 775 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00955 | 0.00927 |
| Ashkenazi Jewish | 0.0000993 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000333 | 0.000308 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000329 | 0.0000327 |
| Other | 0.00219 | 0.00179 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the coat protein complex II (COPII) which promotes the formation of transport vesicles from the endoplasmic reticulum (ER) (PubMed:10788476). The coat has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules (By similarity). {ECO:0000250|UniProtKB:Q9Z2Q1, ECO:0000269|PubMed:10788476}.;
- Disease
- DISEASE: Note=A chromosomal aberration involving SEC31A is associated with inflammatory myofibroblastic tumors (IMTs). Translocation t(2;4)(p23;q21) with ALK.;
- Pathway
- Protein processing in endoplasmic reticulum - Homo sapiens (human);Sterol Regulatory Element-Binding Proteins (SREBP) signalling;XBP1(S) activates chaperone genes;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;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
- 0.136
Intolerance Scores
- loftool
- 0.787
- rvis_EVS
- -0.99
- rvis_percentile_EVS
- 8.63
Haploinsufficiency Scores
- pHI
- 0.390
- hipred
- N
- hipred_score
- 0.476
- ghis
- 0.581
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.913
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sec31a
- Phenotype
Zebrafish Information Network
- Gene name
- sec31a
- Affected structure
- endodermal 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;endoplasmic reticulum to Golgi vesicle-mediated transport;endoplasmic reticulum organization;antigen processing and presentation of exogenous peptide antigen via MHC class II;IRE1-mediated unfolded protein response;COPII vesicle coating;response to calcium ion;COPII-coated vesicle cargo loading;COPII-coated vesicle budding
- Cellular component
- Golgi membrane;cytoplasm;endoplasmic reticulum;endoplasmic reticulum membrane;cytosol;ER to Golgi transport vesicle membrane;vesicle coat;COPII vesicle coat;COPII-coated ER to Golgi transport vesicle;intracellular membrane-bounded organelle;perinuclear region of cytoplasm;endoplasmic reticulum exit site
- Molecular function
- structural molecule activity;protein binding;calcium-dependent protein binding