VTI1A

vesicle transport through interaction with t-SNAREs 1A, the group of SNAREs|MicroRNA protein coding host genes

Basic information

Region (hg38): 10:112446997-112818744

Links

ENSG00000151532 ∙ NCBI:143187 ∙ OMIM:614316 ∙ HGNC:17792 ∙ Uniprot:Q96AJ9 ∙ 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 VTI1A gene.

• Inborn genetic diseases (4 variants)
• Hereditary breast ovarian cancer syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VTI1A 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in VTI1A

This is a list of pathogenic ClinVar variants found in the VTI1A region.

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

Position	Type	Phenotype	Significance	ClinVar
10-112464583-C-T		not specified	Uncertain significance (Jan 03, 2024)
10-112464646-G-A		not specified	Uncertain significance (Aug 17, 2022)
10-112527130-T-C		not specified	Uncertain significance (Mar 29, 2022)
10-112668232-G-A		not specified	Uncertain significance (Apr 22, 2022)
10-112668941-G-A		not specified	Uncertain significance (Apr 18, 2023)
10-112668970-T-C		Hereditary breast ovarian cancer syndrome	Uncertain significance (Aug 01, 2020)
10-112668990-G-A		not specified	Uncertain significance (Feb 15, 2023)
10-112815303-C-T		not specified	Uncertain significance (Jan 23, 2024)
10-112815337-T-G		not specified	Uncertain significance (Feb 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VTI1A	protein_coding	protein_coding	ENST00000393077	8	371748

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000542	0.975	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.160	124	129	0.960	0.00000738	1416
Missense in Polyphen		45	41.75	1.0779		454
Synonymous	0.808	39	46.0	0.848	0.00000253	399
Loss of Function	1.99	8	16.8	0.477	0.00000104	162

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.000272	0.000272
South Asian	0.0000982	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: V-SNARE that mediates vesicle transport pathways through interactions with t-SNAREs on the target membrane. These interactions are proposed to mediate aspects of the specificity of vesicle trafficking and to promote fusion of the lipid bilayers. Involved in vesicular transport from the late endosomes to the trans-Golgi network. Along with VAMP7, involved in an non- conventional RAB1-dependent traffic route to the cell surface used by KCNIP1 and KCND2. May be involved in increased cytokine secretion associated with cellular senescence. {ECO:0000269|PubMed:18195106, ECO:0000269|PubMed:19138172}.
• Pathway: SNARE interactions in vesicular transport - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;Intra-Golgi traffic;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.517
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.195
• hipred: Y
• hipred_score: 0.631
• ghis: 0.645

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.820

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vti1a
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); normal phenotype; reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hearing/vestibular/ear phenotype; 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); vision/eye phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: protein targeting to vacuole;endoplasmic reticulum to Golgi vesicle-mediated transport;intra-Golgi vesicle-mediated transport;Golgi to vacuole transport;autophagy;retrograde transport, endosome to Golgi;vesicle fusion with Golgi apparatus;voluntary musculoskeletal movement;Golgi ribbon formation
• Cellular component: Golgi membrane;endosome;autophagosome;endoplasmic reticulum membrane;Golgi apparatus;cytosol;synaptic vesicle;ER to Golgi transport vesicle membrane;integral component of membrane;clathrin-coated vesicle;SNARE complex;late endosome membrane;trans-Golgi network membrane;neuronal cell body;intracellular membrane-bounded organelle;neuron projection terminus;perinuclear region of cytoplasm
• Molecular function: SNARE binding;SNAP receptor activity;protein binding