CHMP6

charged multivesicular body protein 6, the group of Charged multivesicular body proteins|ESCRT-III

Basic information

Region (hg38): 17:80991597-81009517

Links

ENSG00000176108 ∙ NCBI:79643 ∙ OMIM:610901 ∙ HGNC:25675 ∙ Uniprot:Q96FZ7 ∙ 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 CHMP6 gene.

• Inborn genetic diseases (10 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHMP6 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					1	1
missense			9	1	1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	9	1	3

Variants in CHMP6

This is a list of pathogenic ClinVar variants found in the CHMP6 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-80991953-G-C		not specified	Uncertain significance (Jun 01, 2023)
17-80994609-G-A		not specified	Likely benign (Oct 27, 2021)
17-80994641-G-C		not specified	Uncertain significance (Mar 01, 2023)
17-80994650-C-T		not specified	Uncertain significance (Sep 06, 2022)
17-80994651-G-A		not specified	Uncertain significance (Jul 13, 2021)
17-80994653-G-A		not specified	Uncertain significance (Mar 07, 2024)
17-80994662-C-T		not specified	Uncertain significance (Aug 16, 2021)
17-80994680-G-A			Benign (Dec 31, 2019)
17-80995020-C-T		not specified	Uncertain significance (May 01, 2022)
17-80995081-A-C		not specified	Uncertain significance (Dec 28, 2022)
17-80995727-T-C		not specified	Uncertain significance (Jan 23, 2024)
17-80997010-A-G		not specified	Uncertain significance (Nov 16, 2022)
17-80997047-C-T		not specified	Uncertain significance (Dec 21, 2023)
17-80997071-G-A		not specified	Uncertain significance (Jan 10, 2022)
17-80997264-A-G		not specified	Uncertain significance (Feb 22, 2024)
17-80997348-GC-G			Benign (Oct 19, 2017)
17-80999102-C-T			Benign (Oct 19, 2017)
17-80999116-C-A		not specified	Uncertain significance (Jun 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHMP6	protein_coding	protein_coding	ENST00000325167	8	17920

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.984	0.0164	106653	0	1	106654	0.00000469

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.168	108	113	0.955	0.00000704	1304
Missense in Polyphen		26	36	0.72222		447
Synonymous	0.466	43	47.1	0.914	0.00000320	361
Loss of Function	3.28	0	12.5	0.00	5.32e-7	151

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000103	0.0000103
Middle Eastern	0.00	0.00
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 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. In the ESCRT-III complex, it probably serves as an acceptor for the ESCRT-II complex on endosomal membranes.
• 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: 0.130

Intolerance Scores

• loftool: 0.374
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.04

Haploinsufficiency Scores

• pHI: 0.273
• hipred: Y
• hipred_score: 0.814
• ghis: 0.494

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.884

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Chmp6
• 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)

Zebrafish Information Network

• Gene name: chmp6b
• Affected structure: anatomical system
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: nucleus organization;vacuolar transport;mitotic metaphase plate congression;negative regulation of epidermal growth factor-activated receptor activity;protein transport;endosomal transport;macroautophagy;viral life cycle;multivesicular body assembly;viral budding via host ESCRT complex;regulation of protein catabolic process;midbody abscission;regulation of exosomal secretion;ESCRT III complex assembly
• Cellular component: ESCRT III complex;cytosol;endosome membrane;membrane;late endosome membrane;extracellular exosome
• Molecular function: protein binding;protein-containing complex binding;protein N-terminus binding