CHMP3
charged multivesicular body protein 3, the group of Charged multivesicular body proteins|ESCRT-III
Basic information
Region (hg38): 2:86503430-86563479
Previous symbols: [ "VPS24" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHMP3 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 | 11 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 0 | 0 |
Variants in CHMP3
This is a list of pathogenic ClinVar variants found in the CHMP3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 2-86505929-T-C | not specified | Uncertain significance (May 17, 2023) | ||
| 2-86507545-C-T | not specified | Uncertain significance (Apr 22, 2022) | ||
| 2-86507546-G-T | not specified | Uncertain significance (Oct 29, 2021) | ||
| 2-86529254-T-C | not specified | Uncertain significance (Sep 14, 2023) | ||
| 2-86529271-T-C | not specified | Uncertain significance (Mar 08, 2024) | ||
| 2-86529349-G-A | not specified | Uncertain significance (Jan 31, 2022) | ||
| 2-86529365-A-C | not specified | Uncertain significance (Nov 18, 2022) | ||
| 2-86529388-C-G | not specified | Uncertain significance (Sep 29, 2023) | ||
| 2-86542289-T-C | not specified | Uncertain significance (Mar 07, 2024) | ||
| 2-86542306-C-T | not specified | Uncertain significance (Apr 05, 2023) | ||
| 2-86563309-C-T | not specified | Uncertain significance (Jul 14, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CHMP3 | protein_coding | protein_coding | ENST00000439940 | 6 | 217692 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00400 | 0.963 | 125736 | 0 | 12 | 125748 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.801 | 108 | 134 | 0.805 | 0.00000649 | 1668 |
| Missense in Polyphen | 12 | 22.037 | 0.54454 | 282 | ||
| Synonymous | 0.984 | 36 | 44.3 | 0.812 | 0.00000225 | 434 |
| Loss of Function | 1.86 | 6 | 13.3 | 0.450 | 7.38e-7 | 163 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000877 | 0.0000877 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000163 | 0.000163 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000448 | 0.0000439 |
| Middle Eastern | 0.000163 | 0.000163 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000176 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Probable core component of the endosomal sorting required for transport complex III (ESCRT-III) which is involved in multivesicular bodies (MVBs) formation and sorting of endosomal cargo proteins into MVBs. 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. The MVB pathway appears to require the sequential function of ESCRT-O, -I,-II and -III complexes. ESCRT-III proteins mostly dissociate from the invaginating membrane before the ILV is released. The ESCRT machinery also functions in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and the budding of enveloped viruses (HIV-1 and other lentiviruses). ESCRT-III proteins are believed to mediate the necessary vesicle extrusion and/or membrane fission activities, possibly in conjunction with the AAA ATPase VPS4. Selectively binds to phosphatidylinositol 3,5-bisphosphate PtdIns(3,5)P2 and PtdIns(3,4)P2 in preference to other phosphoinositides tested. Involved in late stages of cytokinesis. Plays a role in endosomal sorting/trafficking of EGF receptor. Isoform 2 prevents stress- mediated cell death and accumulation of reactive oxygen species when expressed in yeast cells. {ECO:0000269|PubMed:14505570, ECO:0000269|PubMed:15707591, ECO:0000269|PubMed:16740483, ECO:0000269|PubMed:17331679, ECO:0000269|PubMed:18076377}.;
- Pathway
- Endocytosis - Homo sapiens (human);Necroptosis - 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;Internalization of ErbB1
(Consensus)
Recessive Scores
- pRec
- 0.108
Intolerance Scores
- loftool
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 33.97
Haploinsufficiency Scores
- pHI
- 0.193
- hipred
- Y
- hipred_score
- 0.672
- ghis
- 0.523
Essentials
- essential_gene_CRISPR
- N
- 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
- Chmp3
- 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);
Gene ontology
- Biological process
- apoptotic process;nucleus organization;mitotic metaphase plate congression;regulation of centrosome duplication;protein transport;endosomal transport;macroautophagy;viral life cycle;endosome transport via multivesicular body sorting pathway;multivesicular body assembly;viral budding via host ESCRT complex;late endosome to vacuole transport;regulation of viral process;protein polymerization;protein heterooligomerization;multivesicular body-lysosome fusion;midbody abscission;multivesicular body sorting pathway;autophagosome maturation;regulation of mitotic spindle assembly;negative regulation of viral release from host cell;positive regulation of viral release from host cell;regulation of exosomal secretion;regulation of early endosome to late endosome transport
- Cellular component
- ESCRT III complex;late endosome;multivesicular body;cytosol;plasma membrane;cytoplasmic vesicle;late endosome membrane;extracellular exosome
- Molecular function
- protein binding;phosphatidylcholine binding;protein homodimerization activity;ubiquitin-specific protease binding