VPS4B
vacuolar protein sorting 4 homolog B, the group of AAA ATPases|ESCRT-IV
Basic information
Region (hg38): 18:63389190-63422483
Previous symbols: [ "SKD1" ]
Links
Phenotypes
GenCC
Source:
- dentin dysplasia type I (Supportive), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the VPS4B 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 | 0 | |||||
| missense | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 0 | 0 |
Variants in VPS4B
This is a list of pathogenic ClinVar variants found in the VPS4B region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 18-63391037-C-T | not specified | Uncertain significance (Nov 17, 2023) | ||
| 18-63391075-G-A | not specified | Uncertain significance (Nov 09, 2023) | ||
| 18-63393468-T-C | not specified | Uncertain significance (Dec 28, 2022) | ||
| 18-63393483-C-G | not specified | Uncertain significance (Feb 15, 2023) | ||
| 18-63393489-A-G | not specified | Uncertain significance (Sep 01, 2021) | ||
| 18-63393501-G-C | not specified | Uncertain significance (Nov 07, 2022) | ||
| 18-63397161-G-A | not specified | Uncertain significance (Jun 27, 2022) | ||
| 18-63397212-G-A | not specified | Uncertain significance (May 25, 2022) | ||
| 18-63400087-C-T | not specified | Uncertain significance (Dec 28, 2023) | ||
| 18-63400143-A-G | not specified | Uncertain significance (Apr 05, 2023) | ||
| 18-63400604-G-A | not specified | Uncertain significance (May 28, 2024) | ||
| 18-63403814-A-G | not specified | Uncertain significance (Mar 25, 2024) | ||
| 18-63407449-A-G | not specified | Uncertain significance (Dec 14, 2022) | ||
| 18-63410334-C-G | not specified | Uncertain significance (Jan 26, 2022) | ||
| 18-63410435-C-T | not specified | Uncertain significance (Jun 06, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| VPS4B | protein_coding | protein_coding | ENST00000238497 | 11 | 33294 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.230 | 0.770 | 125725 | 0 | 23 | 125748 | 0.0000915 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.41 | 133 | 237 | 0.560 | 0.0000123 | 2893 |
| Missense in Polyphen | 47 | 112.94 | 0.41613 | 1374 | ||
| Synonymous | 0.00976 | 85 | 85.1 | 0.999 | 0.00000465 | 848 |
| Loss of Function | 3.50 | 6 | 24.8 | 0.242 | 0.00000140 | 292 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000396 | 0.000396 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000227 | 0.000217 |
| Finnish | 0.0000938 | 0.0000924 |
| European (Non-Finnish) | 0.0000365 | 0.0000352 |
| Middle Eastern | 0.000227 | 0.000217 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in late steps of the endosomal multivesicular bodies (MVB) pathway. Recognizes membrane-associated ESCRT-III assemblies and catalyzes their disassembly, possibly in combination with membrane fission. Redistributes the ESCRT-III components to the cytoplasm for further rounds of MVB sorting. 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. In conjunction with the ESCRT machinery also appears to function in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and enveloped virus budding (HIV-1 and other lentiviruses). VPS4A/B are required for the exosomal release of SDCBP, CD63 and syndecan (PubMed:22660413). {ECO:0000269|PubMed:11563910, ECO:0000269|PubMed:14505570, ECO:0000269|PubMed:18687924, ECO:0000269|PubMed:22660413}.;
- 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;CXCR4-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.156
Intolerance Scores
- loftool
- 0.213
- rvis_EVS
- 0.22
- rvis_percentile_EVS
- 68.13
Haploinsufficiency Scores
- pHI
- 0.443
- hipred
- Y
- hipred_score
- 0.756
- ghis
- 0.503
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.910
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Vps4b
- Phenotype
Zebrafish Information Network
- Gene name
- vps4b
- Affected structure
- ceratobranchial 5 tooth
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- potassium ion transport;nucleus organization;vacuole organization;mitotic metaphase plate congression;regulation of centrosome duplication;positive regulation of G2/M transition of mitotic cell cycle;protein transport;endosomal transport;macroautophagy;viral life cycle;viral release from host cell;cholesterol transport;endosome to lysosome transport via multivesicular body sorting pathway;response to lipid;multivesicular body assembly;viral budding via host ESCRT complex;ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway;positive regulation of viral process;regulation of viral process;protein depolymerization;negative regulation of cell death;late endosomal microautophagy;midbody abscission;ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway;regulation of mitotic spindle assembly;positive regulation of viral release from host cell;negative regulation of exosomal secretion;positive regulation of exosomal secretion;positive regulation of centriole elongation;positive regulation of viral life cycle;ESCRT III complex disassembly
- Cellular component
- spindle pole;nucleus;cytoplasm;endosome;centrosome;cytosol;endosome membrane;late endosome membrane;extracellular exosome;Flemming body
- Molecular function
- protein binding;ATP binding;protein C-terminus binding;ATPase activity;ATPase activity, coupled;identical protein binding;protein homodimerization activity