SEC31B
protein-codingSEC31 homolog B, COPII coat complex component, the group of COPII coat complex|WD repeat domain containing
Gene summary
This gene encodes a protein of unknown function. The protein has moderate similarity to rat VAP1 protein which is an endosomal membrane-associated protein, containing a putative Ca2+/calmodulin-dependent kinase II phosphorylation site. [provided by RefSeq, Jul 2008]
- SEC31L2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~33.2 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 SEC31B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015490.4. 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 | 3 | 1 | 4 | |||
| missense | 180 | 16 | 196 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 184 | 17 | 0 | 201 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_056305.1 | 25 | MANE Select | |
| Ensembl | ENSP00000359370.3 | 25 | MANE Select | |
| Ensembl | ENSP00000474124.1 | 8 | Standard | |
| Ensembl | ENSP00000435359.1 | 8 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| sec31b | Danio rerio | Structure: intestine Quality: decreased size 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
Biological Process
- intracellular protein transport
- endoplasmic reticulum to Golgi vesicle-mediated transport
- endoplasmic reticulum organization
- COPII-coated vesicle cargo loading
- COPII-coated vesicle budding
Molecular Function
- structural molecule activity
Cellular Component
- Golgi membrane
- endoplasmic reticulum membrane
- vesicle coat
- COPII vesicle coat
- endoplasmic reticulum exit site
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000370345
- Coding exons
- 25
- Length
- 43230
- Individuals with no LoFs
- 125392
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 355
- Defined
- 125748
- p
- 0.00142
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0619 | 618 | 622 | 0.993 | 0.0000314 | 7589 |
| Missense (PolyPhen) | 105 | 112.89 | 0.93014 | 1521 | ||
| Synonymous | -0.0785 | 249 | 247 | 1.01 | 0.0000124 | 2434 |
| Loss of Function | 1.22 | 50 | 60.3 | 0.830 | 0.00000289 | 685 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0036 | 0.0036 | notable |
| Latino/Admixed American | 0.0021 | 0.0021 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0037 | 0.0037 | notable |
| Finnish | 0.000047 | 0.000046 | rare |
| European (Non-Finnish) | 0.0011 | 0.0011 | notable |
| South Asian | 0.00095 | 0.00095 | rare |
| Other | 0.00081 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: As a component of the coat protein complex II (COPII), may function in vesicle budding and cargo export from the endoplasmic reticulum. {ECO:0000269|PubMed:16495487}.;
Recessive Scores
- pRec
- 0.0776
Intolerance Scores
- LoFtool
- 0.974
- RVIS EVS
- 2.08
- RVIS percentile EVS
- 97.82
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0500
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |