CHMP7

charged multivesicular body protein 7, the group of Charged multivesicular body proteins|ESCRT-III associated factors

Basic information

Region (hg38): 8:23243637-23262000

Links

ENSG00000147457 ∙ NCBI:91782 ∙ OMIM:611130 ∙ HGNC:28439 ∙ Uniprot:Q8WUX9 ∙ 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 CHMP7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHMP7 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					2	2
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	2

Variants in CHMP7

This is a list of pathogenic ClinVar variants found in the CHMP7 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-23246760-C-T		not specified	Uncertain significance (Mar 21, 2022)
8-23246786-A-C		not specified	Uncertain significance (Oct 05, 2022)
8-23246897-G-T		not specified	Uncertain significance (Jan 10, 2022)
8-23246928-A-T		not specified	Uncertain significance (Apr 15, 2024)
8-23246942-C-T		not specified	Uncertain significance (Nov 10, 2022)
8-23249283-G-T		not specified	Uncertain significance (Jun 02, 2023)
8-23249299-C-T		not specified	Uncertain significance (Mar 20, 2024)
8-23255293-C-T		not specified	Uncertain significance (Apr 15, 2024)
8-23255348-C-G		not specified	Uncertain significance (Apr 08, 2022)
8-23255350-C-T		not specified	Uncertain significance (Dec 26, 2023)
8-23256547-C-G		not specified	Uncertain significance (Feb 15, 2023)
8-23256568-G-A		not specified	Uncertain significance (Jan 26, 2023)
8-23256569-A-T		not specified	Uncertain significance (Nov 08, 2022)
8-23258340-C-T		not specified	Uncertain significance (Feb 23, 2023)
8-23258380-C-T			Benign (Feb 26, 2018)
8-23258387-G-A		not specified	Uncertain significance (Feb 27, 2024)
8-23258427-A-G		not specified	Uncertain significance (Dec 21, 2023)
8-23258786-G-A		not specified	Uncertain significance (Feb 15, 2023)
8-23258812-C-T			Benign (May 21, 2018)
8-23260146-T-A		not specified	Uncertain significance (Mar 14, 2023)
8-23260167-A-G		not specified	Uncertain significance (May 22, 2023)
8-23260254-G-T		not specified	Uncertain significance (Mar 01, 2024)
8-23260321-G-A		not specified	Uncertain significance (May 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHMP7	protein_coding	protein_coding	ENST00000397677	10	18363

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.863	0.137	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.50	191	259	0.737	0.0000141	2925
Missense in Polyphen		26	50.308	0.51682		627
Synonymous	0.0840	103	104	0.990	0.00000539	903
Loss of Function	3.80	4	24.1	0.166	0.00000126	269

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000658	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.0000658	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: ESCRT-III-like protein required to recruit the ESCRT-III complex to the nuclear envelope during late anaphase (PubMed:26040712). Together with SPAST, the ESCRT-III complex promotes nuclear envelope sealing and mitotic spindle disassembly during late anaphase (PubMed:26040712). Plays a role in the endosomal sorting pathway (PubMed:16856878). {ECO:0000269|PubMed:16856878, ECO:0000269|PubMed:26040712}.
• 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: 0.107

Intolerance Scores

• loftool: 0.163
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.63

Haploinsufficiency Scores

• pHI: 0.122
• hipred: Y
• hipred_score: 0.825
• ghis: 0.558

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.855

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chmp7

Gene ontology

• Biological process: nucleus organization;mitotic metaphase plate congression;exit from mitosis;protein transport;endosomal transport;viral life cycle;nuclear envelope reassembly;multivesicular body assembly;viral budding via host ESCRT complex;late endosome to vacuole transport;midbody abscission;protein localization to chromatin;ESCRT III complex disassembly
• Cellular component: chromatin;ESCRT III complex;nucleus;nuclear envelope;cytosol
• Molecular function: protein binding;protein transporter activity