CHMP1B

charged multivesicular body protein 1B, the group of Charged multivesicular body proteins|ESCRT-III associated factors

Basic information

Region (hg38): 18:11851413-11854444

Links

ENSG00000255112 ∙ NCBI:57132 ∙ OMIM:606486 ∙ HGNC:24287 ∙ Uniprot:Q7LBR1 ∙ 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 CHMP1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CHMP1B 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	2
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	1

Variants in CHMP1B

This is a list of pathogenic ClinVar variants found in the CHMP1B region.

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

Position	Type	Phenotype	Significance	ClinVar
18-11851532-C-G		not specified	Uncertain significance (Jun 24, 2022)
18-11851600-A-G		not specified	Uncertain significance (Mar 06, 2023)
18-11851602-G-C		not specified	Uncertain significance (Nov 14, 2023)
18-11851638-G-A		not specified	Uncertain significance (May 31, 2023)
18-11851642-A-G		not specified	Uncertain significance (Oct 29, 2024)
18-11851654-C-G		not specified	Uncertain significance (Oct 22, 2021)
18-11851672-A-G		not specified	Uncertain significance (May 20, 2024)
18-11851681-G-C		not specified	Uncertain significance (Sep 21, 2023)
18-11851686-A-G		not specified	Uncertain significance (Jul 12, 2023)
18-11851696-C-A		not specified	Uncertain significance (Dec 20, 2023)
18-11851728-G-T		not specified	Uncertain significance (Apr 11, 2023)
18-11851780-A-C		not specified	Uncertain significance (Oct 04, 2022)
18-11851814-G-A			Benign (Jun 15, 2018)
18-11851816-C-T		not specified	Uncertain significance (Dec 22, 2023)
18-11851827-A-G		not specified	Uncertain significance (Jan 30, 2024)
18-11851857-G-T		not specified	Uncertain significance (Jun 10, 2024)
18-11851907-G-A		not specified	Uncertain significance (Dec 18, 2023)
18-11851956-G-A		not specified	Uncertain significance (Jun 13, 2023)
18-11851976-A-C		not specified	Uncertain significance (Apr 29, 2024)
18-11852017-C-T		not specified	Uncertain significance (Jun 05, 2024)
18-11852051-G-T			Likely benign (Dec 01, 2020)
18-11852056-C-T		not specified	Uncertain significance (Oct 19, 2024)
18-11852106-G-A		not specified	Uncertain significance (Mar 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CHMP1B	protein_coding	protein_coding	ENST00000526991	1	3054

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.732	0.257	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.257	106	114	0.932	0.00000501	1331
Missense in Polyphen		24	35.748	0.67136		440
Synonymous	0.908	39	46.9	0.831	0.00000220	374
Loss of Function	1.93	0	4.35	0.00	1.85e-7	53

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable peripherally associated 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. Involved in cytokinesis. Involved in recruiting VPS4A and/or VPS4B and SPAST to the midbody of dividing cells. Involved in HIV-1 p6- and p9-dependent virus release. {ECO:0000269|PubMed:14519844, ECO:0000269|PubMed:19129479}.
• Pathway: Endocytosis - Homo sapiens (human);Necroptosis - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.457
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.113
• hipred: N
• hipred_score: 0.476
• ghis: 0.520

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Chmp1b

Gene ontology

• Biological process: nucleus organization;mitotic metaphase plate congression;regulation of centrosome duplication;protein transport;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;cell division;midbody abscission;regulation of mitotic spindle assembly;ESCRT III complex disassembly
• Cellular component: ESCRT III complex;nucleus;multivesicular body;cytosol;endosome membrane;membrane coat;midbody;late endosome membrane;extracellular exosome
• Molecular function: protein binding;protein domain specific binding;identical protein binding