GeneBe

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

ENSG00000119541 ∙ NCBI:9525 ∙ OMIM:609983 ∙ HGNC:10895 ∙ Uniprot:O75351 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • dentin dysplasia type I (Supportive), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VPS4B gene.

  • not_specified (31 variants)

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. These statistics are base on transcript: NM_000004869.4. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
 1
missense
33
clinvar
 33
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
5
clinvar
 5
Total 0 0 39 0 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
VPS4Bprotein_codingprotein_codingENST00000238497 1133294
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.2300.7701257250231257480.0000915
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.411332370.5600.00001232893
Missense in Polyphen47112.940.416131374
Synonymous0.009768585.10.9990.00000465848
Loss of Function3.50624.80.2420.00000140292

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003960.000396
Ashkenazi Jewish0.000.00
East Asian0.0002270.000217
Finnish0.00009380.0000924
European (Non-Finnish)0.00003650.0000352
Middle Eastern0.0002270.000217
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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