| Name | SPATA31 subfamily D, member 5, pseudogene |
| Summary |
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nVarp (VPS9‐ankyrin‐repeat protein), originally characterized as a guanine nucleotide exchange factor (GEF) for Rab21, has been identified as an essential effector for the melanocyte‐specific small GTPases Rab32 and Rab38. In mouse melanocytes, the ANKR1 domain of Varp specifically binds to the active (GTP‐bound) forms of Rab32/38, a binding that is crucial for the proper delivery of tyrosinase-related protein 1 (Tyrp1) to melanosomes, thereby affecting melanogenic enzyme trafficking. This key role in pigment cell biology was revealed by experiments showing that knockdown or misexpression of the Varp ANKR1 domain led to dramatic reductions in peripheral melanosomal Tyrp1 localization."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nVarp’s activity is not limited to melanocytes; it also plays a significant role in regulating endosomal dynamics in other cell types. Acting as a guanine nucleotide exchange factor primarily toward Rab21, Varp localizes primarily to early endosomes, where its functional domains—the VPS9 domain and ankyrin repeats—are required for proper endosomal localization and activity. Disruption of Varp expression perturbs Rab21 function and results in notable alterations of endosome morphology."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": ""}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nFurther dissection of Varp’s molecular functions in melanocytes has uncovered that the binding of Rab32/38, rather than the activation of Rab21 by its VPS9 domain, is essential for Tyrp1 trafficking. Detailed mutagenesis studies have pinpointed critical residues within both Rab32/38 and the ANKR1 domain of Varp that are indispensable for the formation of the functional complex necessary for melanosomal Tyrp1 distribution. Additionally, Varp was shown to interact with the vesicle SNARE VAMP7/TI-VAMP, suggesting that vesicle fusion events are integral to the process. In another regulatory layer, Varp stability is maintained in melanocytes by RACK1, which competes with Rab40C for binding to an alternate ankyrin repeat domain on Varp, ultimately promoting dendrite outgrowth."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": ""}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Kanako Tamura, Norihiko Ohbayashi, Yuto Maruta, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Varp is a novel Rab32/38-binding protein that regulates Tyrp1 trafficking in melanocytes."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Biol Cell (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1091/mbc.e08-12-1161"}], "href": "https://doi.org/10.1091/mbc.e08-12-1161"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19403694"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19403694"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Xinjun Zhang, Xi He, Xin-Yuan Fu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Varp is a Rab21 guanine nucleotide exchange factor and regulates endosome dynamics."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Sci (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1242/jcs.02810"}], "href": "https://doi.org/10.1242/jcs.02810"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16525121"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16525121"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Kanako Tamura, Norihiko Ohbayashi, Koutaro Ishibashi, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Structure-function analysis of VPS9-ankyrin-repeat protein (Varp) in the trafficking of tyrosinase-related protein 1 in melanocytes."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M110.191205"}], "href": "https://doi.org/10.1074/jbc.M110.191205"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21187289"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21187289"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Soujiro Marubashi, Norihiko Ohbayashi, Mitsunori Fukuda "}, {"type": "b", "children": [{"type": "t", "text": "A Varp-Binding Protein, RACK1, Regulates Dendrite Outgrowth through Stabilization of Varp Protein in Mouse Melanocytes."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Invest Dermatol (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.jid.2016.03.034"}], "href": "https://doi.org/10.1016/j.jid.2016.03.034"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "27066885"}], "href": "https://pubmed.ncbi.nlm.nih.gov/27066885"}]}]}]}
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| Synonyms | FAM75D5, FAM75D5P |
| NCBI Gene ID | 347127 |
| API | |
| Download Associations | |
| Predicted Functions |
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| Co-expressed Genes |
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| Expression in Tissues and Cell Lines |
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SPATA31D5P has 203 functional associations with biological entities spanning 4 categories (molecular profile, functional term, phrase or reference, cell line, cell type or tissue, gene, protein or microRNA) extracted from 10 datasets.
Click the + buttons to view associations for SPATA31D5P from the datasets below.
If available, associations are ranked by standardized value
| Dataset | Summary | |
|---|---|---|
| CCLE Cell Line Gene CNV Profiles | cell lines with high or low copy number of SPATA31D5P gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset. | |
| COSMIC Cell Line Gene CNV Profiles | cell lines with high or low copy number of SPATA31D5P gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset. | |
| ENCODE Histone Modification Site Profiles | histone modification site profiles with high histone modification abundance at SPATA31D5P gene from the ENCODE Histone Modification Site Profiles dataset. | |
| ENCODE Transcription Factor Binding Site Profiles | transcription factor binding site profiles with transcription factor binding evidence at the promoter of SPATA31D5P gene from the ENCODE Transcription Factor Binding Site Profiles dataset. | |
| ENCODE Transcription Factor Targets | transcription factors binding the promoter of SPATA31D5P gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset. | |
| GTEx Tissue Gene Expression Profiles | tissues with high or low expression of SPATA31D5P gene relative to other tissues from the GTEx Tissue Gene Expression Profiles dataset. | |
| JASPAR Predicted Transcription Factor Targets | transcription factors regulating expression of SPATA31D5P gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Transcription Factor Targets dataset. | |
| Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles | cell lines with high or low copy number of SPATA31D5P gene relative to other cell lines from the Klijn et al., Nat. Biotechnol., 2015 Cell Line Gene CNV Profiles dataset. | |
| LOCATE Predicted Protein Localization Annotations | cellular components predicted to contain SPATA31D5P protein from the LOCATE Predicted Protein Localization Annotations dataset. | |
| MotifMap Predicted Transcription Factor Targets | transcription factors regulating expression of SPATA31D5P gene predicted using known transcription factor binding site motifs from the MotifMap Predicted Transcription Factor Targets dataset. | |