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.

• not_specified (48 variants)
• not_provided (2 variants)

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. These statistics are base on transcript: NM_000152272.5. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			48			48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	48	0	2

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