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GeneBe

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

ENSG00000152700NCBI:51128OMIM:607690HGNC:10535Uniprot:Q9Y6B6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • chylomicron retention disease (Strong), mode of inheritance: AR
  • chylomicron retention disease (Strong), mode of inheritance: AR
  • chylomicron retention disease (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Chylomicron retention disease (Anderson disease)ARGastrointestinalIndividuals 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 beneficialGastrointestinal; Musculoskeletal; Neurologic2426307; 3792776; 7601203; 10521380; 10665502; 12692552; 17309654; 20920215

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAR1B gene.

  • not provided (106 variants)
  • Inborn genetic diseases (9 variants)
  • Chylomicron retention disease (7 variants)
  • Hereditary pancreatitis (1 variants)
  • SAR1B-related condition (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.

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.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
19
clinvar
1
clinvar
20
missense
1
clinvar
2
clinvar
38
clinvar
41
nonsense
3
clinvar
1
clinvar
4
start loss
0
frameshift
4
clinvar
4
inframe indel
2
clinvar
2
splice donor/acceptor (+/-2bp)
0
splice region
1
1
3
5
non coding
3
clinvar
29
clinvar
4
clinvar
36
Total 8 3 43 48 5

Highest pathogenic variant AF is 0.0000263

Variants in SAR1B

This is a list of pathogenic ClinVar variants found in the SAR1B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
5-134606802-T-C Benign (Sep 22, 2018)1247459
5-134606954-T-G Uncertain significance (Aug 05, 2022)1935024
5-134606956-A-G Likely benign (Dec 06, 2022)1632989
5-134606967-C-A Uncertain significance (May 13, 2022)1993966
5-134606970-T-G Uncertain significance (Sep 27, 2022)1473582
5-134606975-C-T Inborn genetic diseases Uncertain significance (Dec 13, 2023)1409638
5-134606987-C-T Uncertain significance (Sep 19, 2023)1441009
5-134606988-C-T Uncertain significance (Aug 23, 2022)1462385
5-134606988-C-CGTAA Chylomicron retention disease Pathogenic (May 01, 2003)2926
5-134606993-C-A Chylomicron retention disease Pathogenic (Jan 18, 2022)2929
5-134606998-T-C Likely benign (Aug 22, 2022)1955274
5-134607010-A-T Chylomicron retention disease • SAR1B-related condition Likely pathogenic (Jul 24, 2023)2925
5-134607013-A-G Likely benign (Jan 02, 2022)2069869
5-134607027-C-T Uncertain significance (Apr 16, 2022)1964594
5-134607035-C-G Inborn genetic diseases Uncertain significance (Dec 06, 2023)1519644
5-134607035-C-T Uncertain significance (Oct 02, 2022)2200980
5-134607037-G-A Likely benign (Jan 29, 2024)747651
5-134607045-G-A Likely benign (Apr 03, 2021)1565655
5-134607045-G-T Uncertain significance (Jan 19, 2024)1492286
5-134607048-C-A Pathogenic (Jun 25, 2023)2734786
5-134607051-T-G Uncertain significance (May 05, 2022)2133018
5-134607052-C-G Likely benign (Mar 16, 2022)1596303
5-134607069-A-G Inborn genetic diseases Uncertain significance (Oct 24, 2022)1055550
5-134607079-A-G Benign/Likely benign (Jan 19, 2024)1198158
5-134607084-C-A Likely benign (Jan 22, 2024)1647100

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SAR1Bprotein_codingprotein_codingENST00000402673 648128
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.002310.9311257170291257460.000115
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.814831070.7780.000005281283
Missense in Polyphen1634.4420.46455449
Synonymous0.3243638.60.9340.00000211367
Loss of Function1.60612.00.5017.40e-7131

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003490.000349
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.000.00
European (Non-Finnish)0.0001150.000114
Middle Eastern0.0001090.000109
South Asian0.000.00
Other0.0003260.000326

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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