Vacuolar protein sorting-associated protein 13C (VPS13C)
The protein contains 3753 amino acids for an estimated molecular weight of 422390 Da.
Necessary for proper mitochondrial function and maintenance of mitochondrial transmembrane potential. Involved in the regulation of PINK1/PRKN-mediated mitophagy in response to mitochondrial depolarization. (updated: Oct. 25, 2017)
Protein identification was indicated in the following studies:
- Goodman and co-workers. (2013) The proteomics and interactomics of human erythrocytes. Exp Biol Med (Maywood) 238(5), 509-518.
- Lange and co-workers. (2014) Annotating N termini for the human proteome project: N termini and Nα-acetylation status differentiate stable cleaved protein species from degradation remnants in the human erythrocyte proteome. J Proteome Res. 13(4), 2028-2044.
- Hegedűs and co-workers. (2015) Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications. Database (Oxford) 1-8.
- Bryk and co-workers. (2017) Quantitative Analysis of Human Red Blood Cell Proteome. J Proteome Res. 16(8), 2752-2761.
- D'Alessandro and co-workers. (2017) Red blood cell proteomics update: is there more to discover? Blood Transfus. 15(2), 182-187.
- Chu and co-workers. (2018) Quantitative mass spectrometry of human reticulocytes reveal proteome-wide modifications during maturation. Br J Haematol. 180(1), 118-133.
Methods
The following articles were analysed to gather the proteome content of erythrocytes.
The gene or protein list provided in the studies were processed using the ID mapping API of Uniprot in September 2018. The number of proteins identified and mapped without ambiguity in these studies is indicated below.
Only Swiss-Prot entries (reviewed) were considered for protein evidence assignation.
| Publication | Identification 1 | Uniprot mapping 2 | Not mapped / Obsolete | TrEMBL | Swiss-Prot |
|---|---|---|---|---|---|
| Goodman (2013) | 2289 (gene list) | 2278 | 53 | 20599 | 2269 |
| Lange (2014) | 1234 | 1234 | 7 | 28 | 1224 |
| Hegedus (2015) | 2638 | 2622 | 0 | 235 | 2387 |
| Wilson (2016) | 1658 | 1528 | 170 | 291 | 1068 |
| d'Alessandro (2017) | 1826 | 1817 | 2 | 0 | 1815 |
| Bryk (2017) | 2090 | 2060 | 10 | 108 | 1942 |
| Chu (2018) | 1853 | 1804 | 55 | 362 | 1387 |
1 as available in the article and/or in supplementary material
2 uniprot mapping returns all protein isoforms as one entry
The compilation of older studies can be retrieved from the Red Blood Cell Collection database.
The data and differentiation stages presented below come from the proteomic study and analysis performed by our partners of the GReX consortium, more details are available in their published work.
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No binding partner found
Biological Process
Golgi to endosome transport
Mitochondrion organization
Negative regulation of parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization
Protein retention in Golgi apparatus
Protein targeting to vacuole
Response to insulin
Cellular Component
Cytoplasm
Cytosol
Dense core granule membrane
Extracellular exosome
Extrinsic component of membrane
Intracellular anatomical structure
Mitochondrial outer membrane
Obsolete cell
Molecular Function
The reference OMIM entry for this protein is 608879
Vacuolar protein sorting 13, yeast, homolog of, c; vps13c
Kiaa1421
CLONING
By sequencing clones obtained from a size-fractionated adult brain cDNA library, Nagase et al. (2000) cloned VPS13C, which they designated KIAA1421. The deduced protein contains 1,463 amino acids. RT-PCR ELISA detected VPS13C expression in all adult and fetal tissues and all specific brain regions examined. Expression was intermediate in most tissues, but it was lower in adult pancreas and lung and in fetal liver and brain. By searching databases for sequences similar to VPS13A (605978), followed by RT-PCR of lymphoid cell line and brain RNA, Velayos-Baeza et al. (2004) cloned VPS13C. They identified 2 main splice variants, variant 1A and variant 2A, as well as 4 different 3-prime end splice variants. Variant 1A encodes a deduced 3,710-amino acid protein, and variant 2A encodes a deduced 3,753-amino acid protein. VPS13C shares significant similarity with yeast Vps13 and other human VPS13 proteins, mostly in the N and C termini. Northern blot analysis detected expression of variant 1A in all tissues tested, whereas variant 2A was expressed only in brain, although at a higher level than variant 1A.GENE STRUCTURE
Velayos-Baeza et al. (2004) determined that the VPS13C gene contains 86 exons, including 1 alternative exon (exon 81b), and spans 208 kb.MAPPING
Using radiation hybrid analysis, Nagase et al. (2000) mapped the VPS13C gene to chromosome 15. By genomic sequence analysis, Velayos-Baeza et al. (2004) mapped the VPS13C gene to chromosome 15q21.3. They mapped the mouse Vps13c gene to chromosome 9C. ... More on the omim web site
Feb. 10, 2018: Protein entry updated
Automatic update: Entry updated from uniprot information.
Feb. 2, 2018: Protein entry updated
Automatic update: Uniprot description updated
Dec. 19, 2017: Protein entry updated
Automatic update: Uniprot description updated
March 16, 2016: Protein entry updated
Automatic update: OMIM entry 608879 was added.