CHMP2A
charged multivesicular body protein 2A, the group of Charged multivesicular body proteins|ESCRT-III
Basic information
Region (hg38): 19:58551452-58555105
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 CHMP2A 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 | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 0 | 0 |
Variants in CHMP2A
This is a list of pathogenic ClinVar variants found in the CHMP2A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-58551659-C-T | not specified | Uncertain significance (Feb 10, 2022) | ||
| 19-58551660-G-A | not specified | Uncertain significance (Mar 08, 2025) | ||
| 19-58551674-C-T | not specified | Uncertain significance (Jan 21, 2025) | ||
| 19-58551708-C-T | not specified | Uncertain significance (Dec 14, 2024) | ||
| 19-58551752-A-T | not specified | Uncertain significance (Nov 13, 2024) | ||
| 19-58551759-C-G | not specified | Uncertain significance (Sep 29, 2023) | ||
| 19-58552060-C-G | not specified | Uncertain significance (Aug 27, 2024) | ||
| 19-58552108-C-T | not specified | Uncertain significance (Jul 13, 2022) | ||
| 19-58552268-C-T | not specified | Uncertain significance (Nov 05, 2021) | ||
| 19-58552334-C-G | not specified | Uncertain significance (Mar 25, 2024) | ||
| 19-58552350-A-G | not specified | Uncertain significance (Feb 14, 2023) | ||
| 19-58552409-C-G | not specified | Uncertain significance (Jul 12, 2023) | ||
| 19-58554057-C-G | not specified | Uncertain significance (Jan 10, 2023) | ||
| 19-58554133-C-T | not specified | Uncertain significance (Nov 07, 2024) | ||
| 19-58554159-G-C | not specified | Uncertain significance (Nov 25, 2024) | ||
| 19-58554197-C-T | not specified | Uncertain significance (Aug 20, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CHMP2A | protein_coding | protein_coding | ENST00000600118 | 5 | 3559 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.127 | 0.852 | 125738 | 0 | 10 | 125748 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.898 | 110 | 140 | 0.786 | 0.00000879 | 1466 |
| Missense in Polyphen | 35 | 43.762 | 0.79978 | 436 | ||
| Synonymous | -2.31 | 71 | 50.2 | 1.41 | 0.00000262 | 431 |
| Loss of Function | 1.99 | 3 | 9.69 | 0.309 | 5.05e-7 | 112 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.0000993 | 0.0000992 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000616 | 0.0000615 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
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 (PubMed:21310966). Together with SPAST, the ESCRT-III complex promotes nuclear envelope sealing and mitotic spindle disassembly during late anaphase (PubMed:26040712). ESCRT-III proteins are believed to mediate the necessary vesicle extrusion and/or membrane fission activities, possibly in conjunction with the AAA ATPase VPS4. {ECO:0000269|PubMed:21310966, ECO:0000269|PubMed:26040712, ECO:0000305}.;
- Pathway
- Endocytosis - Homo sapiens (human);Necroptosis - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Lysosome Vesicle Biogenesis;Clathrin derived vesicle budding;Disease;trans-Golgi Network Vesicle Budding;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
- 0.130
Intolerance Scores
- loftool
- 0.376
- rvis_EVS
- -0.21
- rvis_percentile_EVS
- 38.28
Haploinsufficiency Scores
- pHI
- 0.130
- hipred
- Y
- hipred_score
- 0.785
- ghis
- 0.614
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.965
Mouse Genome Informatics
- Gene name
- Chmp2a
- Phenotype
Zebrafish Information Network
- Gene name
- chmp2a
- Affected structure
- trunk
- Phenotype tag
- abnormal
- Phenotype quality
- necrotic
Gene ontology
- Biological process
- nucleus organization;mitotic metaphase plate congression;membrane invagination;exit from mitosis;regulation of centrosome duplication;protein transport;endosomal transport;macroautophagy;viral life cycle;nuclear envelope reassembly;endosome transport via multivesicular body sorting pathway;multivesicular body assembly;viral budding via host ESCRT complex;establishment of protein localization;late endosome to vacuole transport;regulation of viral process;protein polymerization;protein homooligomerization;protein heterooligomerization;negative regulation of cell death;midbody abscission;regulation of mitotic spindle assembly;positive regulation of viral release from host cell;positive regulation of exosomal secretion;negative regulation of centriole elongation;ESCRT III complex disassembly
- Cellular component
- chromatin;ESCRT III complex;nuclear envelope;multivesicular body;cytosol;membrane;membrane coat;late endosome membrane;extracellular exosome
- Molecular function
- protein binding;protein domain specific binding;phosphatidylcholine binding