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

ENSG00000152700 ∙ NCBI:51128 ∙ OMIM:607690 ∙ HGNC:10535 ∙ Uniprot:Q9Y6B6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

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 ClinVar and linked to the SAR1B gene.

• not provided (6 variants)
• Inborn genetic diseases (2 variants)
• Chylomicron retention disease (2 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				22	1	23
missense	1	2	42			45
nonsense	3	1				4
start loss						0
frameshift	4					4
inframe indel			2			2
splice donor/acceptor (+/-2bp)						0
splice region			1	4	3	8
non coding			3	37	4	44
Total	8	3	47	59	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)
5-134606954-T-G			Uncertain significance (Aug 05, 2022)
5-134606956-A-G			Likely benign (Dec 06, 2022)
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 (Dec 13, 2023)
5-134606987-C-T			Uncertain significance (Sep 19, 2023)
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 • SAR1B-related disorder	Likely pathogenic (Jul 24, 2023)
5-134607013-A-G			Likely benign (Jan 02, 2022)
5-134607027-C-T			Uncertain significance (Apr 16, 2022)
5-134607035-C-G		Inborn genetic diseases	Uncertain significance (Dec 06, 2023)
5-134607035-C-T			Uncertain significance (Oct 02, 2022)
5-134607037-G-A			Likely benign (Jan 29, 2024)
5-134607045-G-A			Likely benign (Apr 03, 2021)
5-134607045-G-T			Uncertain significance (Jan 19, 2024)
5-134607048-C-A			Pathogenic (Jun 25, 2023)
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 (Jan 19, 2024)
5-134607084-C-A			Likely benign (Jan 22, 2024)

GnomAD

Source: gnomAD

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: 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

	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