VMP1

vacuole membrane protein 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 17:59707192-59842255

Previous symbols: [ "TMEM49" ]

Links

ENSG00000062716 ∙ NCBI:81671 ∙ OMIM:611753 ∙ HGNC:29559 ∙ Uniprot:Q96GC9 ∙ 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 VMP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VMP1 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			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	0

Variants in VMP1

This is a list of pathogenic ClinVar variants found in the VMP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-59707386-T-C		not specified	Likely benign (Feb 06, 2018)
17-59707387-C-T		not specified	Likely benign (Aug 31, 2016)
17-59707388-C-T		not specified	Likely benign (Mar 01, 2018)
17-59707395-G-A		not specified	Likely benign (Feb 16, 2018)
17-59707403-C-T		not specified	Likely benign (Oct 09, 2017)
17-59707407-C-T		not specified	Likely benign (Mar 07, 2016)
17-59707411-T-C		not specified	Likely benign (Aug 01, 2017)
17-59707607-G-T			Benign (Dec 01, 2021)
17-59731498-G-A		not specified	Uncertain significance (Jun 13, 2024)
17-59735426-G-T		not specified	Uncertain significance (Oct 04, 2022)
17-59738862-TTC-T		Monoclonal B-Cell Lymphocytosis	Uncertain significance (Dec 15, 2015)
17-59765041-A-G		not specified	Uncertain significance (Feb 02, 2022)
17-59765085-A-G		not specified	Likely benign (Feb 22, 2023)
17-59811704-C-T		not specified	Uncertain significance (Dec 05, 2022)
17-59838386-G-T		not specified	Uncertain significance (Nov 19, 2022)
17-59839784-C-T		not specified	Uncertain significance (Dec 19, 2023)
17-59839807-G-A		not specified	Uncertain significance (Dec 15, 2021)
17-59839831-C-G		not specified	Uncertain significance (Apr 12, 2023)
17-59839837-A-C		not specified	Uncertain significance (Mar 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VMP1	protein_coding	protein_coding	ENST00000262291	11	135064

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.963	0.0373	125739	0	6	125745	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.25	126	220	0.573	0.0000110	2651
Missense in Polyphen		15	68.745	0.2182		821
Synonymous	1.09	64	76.2	0.840	0.00000386	764
Loss of Function	3.92	3	23.5	0.128	9.93e-7	293

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000244	0.000242
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000882	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Stress-induced protein that, when overexpressed, promotes formation of intracellular vacuoles followed by cell death. May be involved in the cytoplasmic vacuolization of acinar cells during the early stage of acute pancreatitis. Plays a role in the initial stages of the autophagic process through its interaction with BECN1 (By similarity). Involved in cell-cell adhesion. Plays an essential role in formation of cell junctions (PubMed:17724469). Required for autophagosome formation (PubMed:30093494). {ECO:0000250|UniProtKB:Q91ZQ0, ECO:0000269|PubMed:17724469, ECO:0000269|PubMed:30093494}.
• Pathway: Autophagy - animal - Homo sapiens (human);Nanoparticle triggered autophagic cell death (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.525
• hipred: Y
• hipred_score: 0.728
• ghis: 0.611

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vmp1

Zebrafish Information Network

• Gene name: vmp1
• Affected structure: hepatocyte
• Phenotype tag: abnormal
• Phenotype quality: increased size

Gene ontology

• Biological process: autophagosome assembly;autophagy;Golgi organization;embryo implantation;cell junction assembly;cell-cell adhesion
• Cellular component: phagophore assembly site;autophagosome membrane;nucleolus;endoplasmic reticulum;plasma membrane;integral component of membrane;endoplasmic reticulum-Golgi intermediate compartment membrane
• Molecular function: protein binding