VMP1
Basic information
Region (hg38): 17:59707192-59842255
Previous symbols: [ "TMEM49" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (22 variants)
- Monoclonal_B-Cell_Lymphocytosis (1 variants)
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. These statistics are base on transcript: NM_000030938.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 20 | 22 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 21 | 2 | 0 |
GnomAD
Source:
| 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:
- 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
- loftool
- 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
- Phenotype
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