USE1

unconventional SNARE in the ER 1, the group of SNAREs

Basic information

Region (hg38): 19:17215346-17220237

Links

ENSG00000053501 ∙ NCBI:55850 ∙ OMIM:610675 ∙ HGNC:30882 ∙ Uniprot:Q9NZ43 ∙ 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 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			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)
19-17215463-A-G		not specified	Uncertain significance (Nov 10, 2024)
19-17215482-A-G		not specified	Uncertain significance (Jun 19, 2024)
19-17215827-T-G		not specified	Uncertain significance (Jun 27, 2022)
19-17215841-G-A		not specified	Uncertain significance (Dec 05, 2024)
19-17216170-C-T		not specified	Uncertain significance (Nov 12, 2021)
19-17216301-C-T		not specified	Uncertain significance (Dec 28, 2022)
19-17216317-G-A		not specified	Uncertain significance (Jun 11, 2024)
19-17216320-C-T		not specified	Uncertain significance (Nov 07, 2024)
19-17217457-C-G		not specified	Uncertain significance (Oct 27, 2022)
19-17218378-G-A		not specified	Uncertain significance (Sep 22, 2021)
19-17219257-C-T		not specified	Uncertain significance (Jan 24, 2023)
19-17219275-T-G		not specified	Uncertain significance (Sep 12, 2023)
19-17219308-C-T		not specified	Uncertain significance (Feb 27, 2023)
19-17219358-G-A		not specified	Uncertain significance (Apr 24, 2024)
19-17219383-A-G		not specified	Uncertain significance (Aug 28, 2024)
19-17219642-C-G		not specified	Uncertain significance (Jun 09, 2022)
19-17219683-C-G		not specified	Uncertain significance (Dec 20, 2021)
19-17219694-C-T		not specified	Uncertain significance (May 23, 2024)
19-17219695-G-A		not specified	Uncertain significance (Feb 22, 2023)
19-17219740-C-T		not specified	Uncertain significance (May 08, 2024)
19-17219748-A-T		not specified	Uncertain significance (Aug 04, 2021)
19-17219781-C-T		not specified	Uncertain significance (Oct 05, 2021)
19-17219785-T-G		not specified	Uncertain significance (Mar 18, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USE1	protein_coding	protein_coding	ENST00000263897	8	4484

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000207	0.908	124937	0	32	124969	0.000128

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.516	137	155	0.883	0.00000923	1630
Missense in Polyphen		39	45.243	0.862		498
Synonymous	0.498	60	65.1	0.921	0.00000389	515
Loss of Function	1.59	10	17.1	0.586	9.92e-7	175

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000251	0.000242
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000170	0.000168
Middle Eastern	0.000111	0.000111
South Asian	0.0000654	0.0000654
Other	0.000336	0.000328

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

• 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

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

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