CHMP5
charged multivesicular body protein 5, the group of Charged multivesicular body proteins|ESCRT-III associated factors
Basic information
Region (hg38): 9:33264879-33282070
Previous symbols: [ "C9orf83", "SNF7DC2" ]
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 CHMP5 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 | 12 | ||||
| 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 | 1 | 0 |
Variants in CHMP5
This is a list of pathogenic ClinVar variants found in the CHMP5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-33265088-C-T | not specified | Likely benign (Dec 28, 2023) | ||
| 9-33265146-C-T | not specified | Uncertain significance (May 30, 2023) | ||
| 9-33266077-A-C | not specified | Uncertain significance (Apr 22, 2022) | ||
| 9-33266092-A-G | not specified | Uncertain significance (Jan 19, 2022) | ||
| 9-33270636-C-T | not specified | Uncertain significance (Sep 17, 2021) | ||
| 9-33271184-G-T | not specified | Uncertain significance (Jan 24, 2023) | ||
| 9-33276472-T-C | Uncertain significance (Aug 01, 2019) | |||
| 9-33276474-G-A | not specified | Uncertain significance (Dec 21, 2022) | ||
| 9-33276474-G-C | not specified | Uncertain significance (Nov 03, 2022) | ||
| 9-33276496-A-G | not specified | Uncertain significance (Sep 27, 2021) | ||
| 9-33276560-A-T | not specified | Uncertain significance (Feb 27, 2024) | ||
| 9-33278155-G-A | not specified | Uncertain significance (Oct 30, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CHMP5 | protein_coding | protein_coding | ENST00000223500 | 8 | 17038 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00665 | 0.977 | 125733 | 0 | 15 | 125748 | 0.0000596 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.735 | 95 | 117 | 0.809 | 0.00000561 | 1453 |
| Missense in Polyphen | 27 | 35.476 | 0.76107 | 475 | ||
| Synonymous | -0.471 | 44 | 40.2 | 1.09 | 0.00000183 | 384 |
| Loss of Function | 2.10 | 6 | 14.7 | 0.409 | 7.72e-7 | 174 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000661 | 0.000653 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000880 | 0.00000879 |
| Middle Eastern | 0.000661 | 0.000653 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Probable peripherally associated 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. Involved in HIV-1 p6- and p9-dependent virus release. {ECO:0000269|PubMed:14519844}.;
- 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
(Consensus)
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- 0.349
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.2
Haploinsufficiency Scores
- pHI
- 0.721
- hipred
- Y
- hipred_score
- 0.765
- ghis
- 0.674
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Chmp5
- Phenotype
- embryo 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); 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); 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); growth/size/body region phenotype; cellular phenotype;
Gene ontology
- Biological process
- regulation of receptor recycling;nucleus organization;lysosome organization;mitotic metaphase plate congression;endosome to lysosome transport;regulation of centrosome duplication;protein transport;viral life cycle;multivesicular body assembly;viral budding;midbody abscission;cellular response to lipopolysaccharide;cellular response to muramyl dipeptide;multivesicular body sorting pathway;regulation of mitotic spindle assembly;ESCRT III complex disassembly
- Cellular component
- nucleus;cytosol;endosome membrane;extracellular exosome
- Molecular function
- protein binding;cadherin binding