CHMP2A

charged multivesicular body protein 2A, the group of Charged multivesicular body proteins|ESCRT-III

Basic information

Region (hg38): 19:58551452-58555105

Links

ENSG00000130724

∙ NCBI:27243 ∙ OMIM:610893 ∙ HGNC:30216 ∙ Uniprot:O43633 ∙ 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 CHMP2A gene.

not_specified (22 variants)

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. These statistics are base on transcript: NM_000014453.4. 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			22 clinvar			22
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	22	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

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: dbNSFP

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