SAR1A

secretion associated Ras related GTPase 1A, the group of COPII coat complex|ARF GTPase family

Basic information

Region (hg38): 10:70147288-70170523

Previous symbols: [ "SARA1" ]

Links

ENSG00000079332 ∙ NCBI:56681 ∙ OMIM:607691 ∙ HGNC:10534 ∙ Uniprot:Q9NR31 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAR1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAR1A 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						0
missense			1	1		2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	1	0

Variants in SAR1A

This is a list of pathogenic ClinVar variants found in the SAR1A region.

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

Position	Type	Phenotype	Significance	ClinVar
10-70153933-T-C		not specified	Uncertain significance (Mar 31, 2022)
10-70157787-C-T		not specified	Likely benign (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAR1A	protein_coding	protein_coding	ENST00000373242	6	23235

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.372	0.618	125448	0	14	125462	0.0000558

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.09	51	114	0.448	0.00000625	1301
Missense in Polyphen		8	36.07	0.22179		455
Synonymous	1.51	27	39.0	0.692	0.00000211	371
Loss of Function	2.16	2	9.01	0.222	3.77e-7	119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000597	0.000597
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in transport from the endoplasmic reticulum to the Golgi apparatus (By similarity). Required to maintain SEC16A localization at discrete locations on the ER membrane perhaps by preventing its dissociation. SAR1A-GTP-dependent assembly of SEC16A on the ER membrane forms an organized scaffold defining endoplasmic reticulum exit sites (ERES). {ECO:0000250, ECO:0000269|PubMed:17005010}.
• Pathway: Legionellosis - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);Sterol Regulatory Element-Binding Proteins (SREBP) signalling;tgf beta signaling pathway (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.185
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

• pHI: 0.485
• hipred: Y
• hipred_score: 0.617
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Low	Medium
Primary Immunodeficiency	Medium	Low	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Sar1a

Gene ontology

• Biological process: regulation of COPII vesicle coating;intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;vesicle organization;membrane organization;positive regulation of protein exit from endoplasmic reticulum;COPII-coated vesicle cargo loading
• Cellular component: Golgi membrane;endoplasmic reticulum;COPII vesicle coat;endoplasmic reticulum exit site
• Molecular function: GTPase activity;protein binding;GTP binding