VPS25
Basic information
Region (hg38): 17:42773449-42779599
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (15 variants)
- VPS25-related_neurodevelopmental_delay (3 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the VPS25 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000032353.4. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 15 | 18 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 2 | 15 | 0 | 1 |
Highest pathogenic variant AF is 0.000016727132
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| VPS25 | protein_coding | protein_coding | ENST00000253794 | 6 | 6164 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0776 | 0.912 | 125739 | 0 | 9 | 125748 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.48 | 59 | 101 | 0.585 | 0.00000530 | 1159 |
| Missense in Polyphen | 15 | 37.049 | 0.40487 | 417 | ||
| Synonymous | -0.516 | 47 | 42.7 | 1.10 | 0.00000248 | 314 |
| Loss of Function | 2.24 | 4 | 12.6 | 0.317 | 5.50e-7 | 126 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000139 | 0.000139 |
| European (Non-Finnish) | 0.0000352 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the ESCRT-II complex (endosomal sorting complex required for transport II), which is required for multivesicular body (MVB) formation and sorting of endosomal cargo proteins into MVBs. The MVB pathway mediates delivery of transmembrane proteins into the lumen of the lysosome for degradation. The ESCRT-II complex is probably involved in the recruitment of the ESCRT-III complex. The ESCRT-II complex may also play a role in transcription regulation, possibly via its interaction with ELL. The ESCRT-II complex may be involved in facilitating the budding of certain RNA viruses. {ECO:0000269|PubMed:18723511}.;
- Pathway
- Endocytosis - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;Endosomal Sorting Complex Required For Transport (ESCRT)
(Consensus)
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- loftool
- 0.398
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 59.76
Haploinsufficiency Scores
- pHI
- 0.544
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.598
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.958
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Vps25
- Phenotype
- growth/size/body region phenotype; craniofacial phenotype; cellular phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; skeleton phenotype;
Gene ontology
- Biological process
- negative regulation of epidermal growth factor-activated receptor activity;endosomal transport;macroautophagy;multivesicular body assembly;protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
- Cellular component
- ESCRT II complex;nucleus;nucleoplasm;cytoplasm;cytosol;endosome membrane;extracellular exosome
- Molecular function
- structural molecule activity;protein binding;protein homodimerization activity;protein N-terminus binding