VTA1

vesicle trafficking 1, the group of ESCRT-IV

Basic information

Region (hg38): 6:142147162-142224685

Previous symbols: [ "C6orf55" ]

Links

ENSG00000009844 ∙ NCBI:51534 ∙ OMIM:610902 ∙ HGNC:20954 ∙ Uniprot:Q9NP79 ∙ 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 VTA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VTA1 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			17			17
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	17	0	0

Variants in VTA1

This is a list of pathogenic ClinVar variants found in the VTA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-142147300-G-A		not specified	Uncertain significance (Jul 25, 2023)
6-142147339-C-T		not specified	Likely pathogenic (Mar 17, 2024)
6-142166264-A-G		not specified	Uncertain significance (Aug 16, 2021)
6-142166275-C-T		not specified	Uncertain significance (Oct 12, 2021)
6-142166284-C-T		not specified	Uncertain significance (Mar 22, 2022)
6-142166285-G-A		not specified	Uncertain significance (Oct 29, 2021)
6-142169560-A-G		not specified	Uncertain significance (May 25, 2023)
6-142169659-G-A		not specified	Uncertain significance (Nov 01, 2022)
6-142170374-A-C		not specified	Uncertain significance (Dec 20, 2023)
6-142170392-A-G		not specified	Uncertain significance (Feb 28, 2023)
6-142189472-A-G		not specified	Uncertain significance (Oct 12, 2021)
6-142198459-G-A		not specified	Uncertain significance (Mar 19, 2024)
6-142198478-C-G		not specified	Uncertain significance (May 30, 2023)
6-142204003-T-C		not specified	Uncertain significance (Jan 08, 2024)
6-142204041-G-A		not specified	Uncertain significance (Nov 18, 2022)
6-142204041-G-T		not specified	Uncertain significance (Feb 28, 2023)
6-142218506-C-T		not specified	Uncertain significance (Nov 03, 2023)
6-142218519-A-T		not specified	Uncertain significance (Nov 18, 2022)
6-142218627-C-T		not specified	Uncertain significance (May 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VTA1	protein_coding	protein_coding	ENST00000367630	8	77460

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000399	0.963	125726	0	18	125744	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.315	181	169	1.07	0.00000846	2003
Missense in Polyphen		61	69.357	0.87951		827
Synonymous	-0.832	69	60.7	1.14	0.00000313	584
Loss of Function	1.85	8	16.0	0.500	7.63e-7	204

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000244	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000112	0.000105
Middle Eastern	0.000244	0.000217
South Asian	0.0000335	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the endosomal multivesicular bodies (MVB) pathway. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. Thought to be a cofactor of VPS4A/B, which catalyzes disassembles membrane-associated ESCRT-III assemblies. Involved in the sorting and down-regulation of EGFR (By similarity). Involved in HIV-1 budding. {ECO:0000250, ECO:0000269|PubMed:15644320}.
• Pathway: Endocytosis - Homo sapiens (human);Disease;Vesicle-mediated transport;Membrane Trafficking;Budding and maturation of HIV virion;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;Endosomal Sorting Complex Required For Transport (ESCRT);Infectious disease (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.702
• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.25

Haploinsufficiency Scores

• pHI: 0.386
• hipred: Y
• hipred_score: 0.613
• ghis: 0.512

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.942

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vta1

Gene ontology

• Biological process: protein transport;macroautophagy;viral life cycle;multivesicular body assembly;viral budding;multivesicular body sorting pathway;ESCRT III complex disassembly
• Cellular component: nucleoplasm;cytosol;endosome membrane;intracellular membrane-bounded organelle;extracellular exosome
• Molecular function: protein binding;protein C-terminus binding