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GeneBe

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

ENSG00000079332NCBI:56681OMIM:607691HGNC:10534Uniprot:Q9NR31AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

  • Inborn genetic diseases (1 variants)

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
clinvar
1
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 0 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 Inborn genetic diseases Uncertain significance (Mar 31, 2022)2354347

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SAR1Aprotein_codingprotein_codingENST00000373242 623235
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.3720.6181254480141254620.0000558
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.09511140.4480.000006251301
Missense in Polyphen836.070.22179455
Synonymous1.512739.00.6920.00000211371
Loss of Function2.1629.010.2223.77e-7119

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0005970.000597
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

AllRecessiveDominant
MendelianMediumLowMedium
Primary ImmunodeficiencyMediumLowMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sar1a
Phenotype

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