USE1

unconventional SNARE in the ER 1, the group of SNAREs

Basic information

Region (hg38): 19:17215346-17220237

Links

ENSG00000053501NCBI:55850OMIM:610675HGNC:30882Uniprot:Q9NZ43AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the USE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USE1 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
24
clinvar
24
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 24 0 0

Variants in USE1

This is a list of pathogenic ClinVar variants found in the USE1 region.

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

Position Type Phenotype Significance ClinVar
19-17215460-G-A not specified Uncertain significance (Dec 21, 2022)2337925
19-17215463-A-G not specified Uncertain significance (Nov 10, 2024)3466501
19-17215482-A-G not specified Uncertain significance (Jun 19, 2024)3331259
19-17215827-T-G not specified Uncertain significance (Jun 27, 2022)2298019
19-17215841-G-A not specified Uncertain significance (Dec 05, 2024)3466503
19-17216170-C-T not specified Uncertain significance (Nov 12, 2021)2260574
19-17216301-C-T not specified Uncertain significance (Dec 28, 2022)2211900
19-17216317-G-A not specified Uncertain significance (Jun 11, 2024)2411881
19-17216320-C-T not specified Uncertain significance (Nov 07, 2024)2397423
19-17217457-C-G not specified Uncertain significance (Oct 27, 2022)2354447
19-17218378-G-A not specified Uncertain significance (Sep 22, 2021)2360826
19-17219257-C-T not specified Uncertain significance (Jan 24, 2023)2471809
19-17219275-T-G not specified Uncertain significance (Sep 12, 2023)2623006
19-17219308-C-T not specified Uncertain significance (Feb 27, 2023)2463813
19-17219358-G-A not specified Uncertain significance (Apr 24, 2024)3331256
19-17219383-A-G not specified Uncertain significance (Aug 28, 2024)3466500
19-17219642-C-G not specified Uncertain significance (Jun 09, 2022)2221105
19-17219683-C-G not specified Uncertain significance (Dec 20, 2021)2268091
19-17219694-C-T not specified Uncertain significance (May 23, 2024)3331258
19-17219695-G-A not specified Uncertain significance (Feb 22, 2023)2466755
19-17219740-C-T not specified Uncertain significance (May 08, 2024)3331257
19-17219748-A-T not specified Uncertain significance (Aug 04, 2021)2345439
19-17219781-C-T not specified Uncertain significance (Oct 05, 2021)2375473
19-17219785-T-G not specified Uncertain significance (Mar 18, 2024)3331255

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
USE1protein_codingprotein_codingENST00000263897 84484
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00002070.9081249370321249690.000128
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.5161371550.8830.000009231630
Missense in Polyphen3945.2430.862498
Synonymous0.4986065.10.9210.00000389515
Loss of Function1.591017.10.5869.92e-7175

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002510.000242
Ashkenazi Jewish0.000.00
East Asian0.0001110.000111
Finnish0.00004640.0000464
European (Non-Finnish)0.0001700.000168
Middle Eastern0.0001110.000111
South Asian0.00006540.0000654
Other0.0003360.000328

dbNSFP

Source: dbNSFP

Function
FUNCTION: SNARE that may be involved in targeting and fusion of Golgi-derived retrograde transport vesicles with the ER. {ECO:0000269|PubMed:15272311}.;
Pathway
SNARE interactions in vesicular transport - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

pRec
0.113

Intolerance Scores

loftool
rvis_EVS
-0.27
rvis_percentile_EVS
33.97

Haploinsufficiency Scores

pHI
0.136
hipred
N
hipred_score
0.491
ghis
0.584

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.925

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Use1
Phenotype
cellular phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process
endoplasmic reticulum to Golgi vesicle-mediated transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;lysosomal transport;protein transport;protein catabolic process;secretion by cell
Cellular component
lysosome;endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
Molecular function
protein binding