SAR1B
secretion associated Ras related GTPase 1B, the group of ARF GTPase family|COPII coat complex
Basic information
Region (hg38): 5:134601148-134649271
Previous symbols: [ "SARA2" ]
Links
Phenotypes
GenCC
Source:
- chylomicron retention disease (Strong), mode of inheritance: AR
- chylomicron retention disease (Supportive), mode of inheritance: AR
- chylomicron retention disease (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Chylomicron retention disease (Anderson disease) | AR | Gastrointestinal | Individuals typically present in infancy with with steatorrhea and failure to thrive, and dietary measures (maintenance of adequate caloric intake on a low-long chain fat diet consisting of polyunsaturated fatty acids, with supplementation of lipid soluble vitamins, including large amounts of vitamin E, and essential fatty acids) can be beneficial | Gastrointestinal; Musculoskeletal; Neurologic | 2426307; 3792776; 7601203; 10521380; 10665502; 12692552; 17309654; 20920215 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (103 variants)
- Chylomicron retention disease (12 variants)
- Inborn genetic diseases (9 variants)
- Hereditary pancreatitis (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAR1B gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 19 | 1 | 20 | |||
| missense | 2 | 1 | 39 | 42 | ||
| nonsense | 3 | 1 | 4 | |||
| start loss | 0 | |||||
| frameshift | 3 | 2 | 5 | |||
| inframe indel | 3 | 3 | ||||
| splice variant | 2 | 1 | 3 | 2 | 8 | |
| non coding | 1 | 27 | 4 | 32 | ||
| Total | 13 | 2 | 43 | 49 | 7 |
Highest pathogenic variant AF is 0.0000263
Variants in SAR1B
This is a list of pathogenic ClinVar variants found in the SAR1B region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-134606802-T-C | Benign (Sep 22, 2018) | |||
| 5-134606954-T-G | Uncertain significance (Aug 05, 2022) | |||
| 5-134606956-A-G | Likely benign (Oct 21, 2021) | |||
| 5-134606967-C-A | Uncertain significance (May 13, 2022) | |||
| 5-134606970-T-G | Uncertain significance (Sep 27, 2022) | |||
| 5-134606975-C-T | Inborn genetic diseases | Uncertain significance (Aug 20, 2021) | ||
| 5-134606987-C-T | Uncertain significance (Dec 27, 2021) | |||
| 5-134606988-C-T | Uncertain significance (Aug 23, 2022) | |||
| 5-134606988-C-CGTAA | Chylomicron retention disease | Pathogenic (May 01, 2003) | ||
| 5-134606993-C-A | Chylomicron retention disease | Pathogenic (Jan 18, 2022) | ||
| 5-134606998-T-C | Likely benign (Aug 22, 2022) | |||
| 5-134607010-A-T | Chylomicron retention disease | Pathogenic (Jan 01, 2008) | ||
| 5-134607013-A-G | Likely benign (Jan 02, 2022) | |||
| 5-134607027-C-T | Uncertain significance (Apr 16, 2022) | |||
| 5-134607035-C-G | Uncertain significance (Aug 16, 2022) | |||
| 5-134607035-C-T | Uncertain significance (Oct 02, 2022) | |||
| 5-134607037-G-A | Likely benign (Oct 18, 2022) | |||
| 5-134607045-G-A | Likely benign (Apr 03, 2021) | |||
| 5-134607045-G-T | Uncertain significance (Jan 27, 2022) | |||
| 5-134607051-T-G | Uncertain significance (May 05, 2022) | |||
| 5-134607052-C-G | Likely benign (Mar 16, 2022) | |||
| 5-134607069-A-G | Inborn genetic diseases | Uncertain significance (Oct 24, 2022) | ||
| 5-134607079-A-G | Benign/Likely benign (Nov 01, 2022) | |||
| 5-134607084-C-A | Likely benign (Sep 07, 2022) | |||
| 5-134608167-C-G | Benign (Apr 04, 2019) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SAR1B | protein_coding | protein_coding | ENST00000402673 | 6 | 48128 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00231 | 0.931 | 125717 | 0 | 29 | 125746 | 0.000115 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.814 | 83 | 107 | 0.778 | 0.00000528 | 1283 |
| Missense in Polyphen | 16 | 34.442 | 0.46455 | 449 | ||
| Synonymous | 0.324 | 36 | 38.6 | 0.934 | 0.00000211 | 367 |
| Loss of Function | 1.60 | 6 | 12.0 | 0.501 | 7.40e-7 | 131 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000349 | 0.000349 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000115 | 0.000114 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in transport from the endoplasmic reticulum to the Golgi apparatus. Activated by the guanine nucleotide exchange factor PREB. Involved in the selection of the protein cargo and the assembly of the COPII coat complex.;
- Pathway
- Legionellosis - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);Sterol Regulatory Element-Binding Proteins (SREBP) signalling;Chylomicron assembly;Vesicle-mediated transport;Plasma lipoprotein assembly;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;MHC class II antigen presentation;Immune System;Adaptive Immune System;Transport of small molecules;Class I MHC mediated antigen processing & presentation;Cargo concentration in the ER;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Plasma lipoprotein assembly, remodeling, and clearance;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport;Antigen Presentation: Folding, assembly and peptide loading of class I MHC
(Consensus)
Recessive Scores
- pRec
- 0.142
Intolerance Scores
- loftool
- 0.458
- rvis_EVS
- -0.23
- rvis_percentile_EVS
- 36.86
Haploinsufficiency Scores
- pHI
- 0.457
- hipred
- N
- hipred_score
- 0.292
- ghis
- 0.661
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.398
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sar1b
- Phenotype
- hematopoietic system phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- sar1b
- Affected structure
- rhombic lip
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- antigen processing and presentation of peptide antigen via MHC class I;regulation of COPII vesicle coating;intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;vesicle organization;antigen processing and presentation of exogenous peptide antigen via MHC class II;COPII vesicle coating;membrane organization;positive regulation of protein exit from endoplasmic reticulum
- Cellular component
- endoplasmic reticulum;endoplasmic reticulum membrane;cytosol;ER to Golgi transport vesicle membrane;COPII vesicle coat;Golgi cisterna membrane;endoplasmic reticulum exit site
- Molecular function
- GTPase activity;GTP binding;metal ion binding