VPS13D Gene

Name	vacuolar protein sorting 13 homolog D (S. cerevisiae)
Description	This gene encodes a protein belonging to the vacuolar-protein-sorting-13 gene family. In yeast, vacuolar-protein-sorting-13 proteins are involved in trafficking of membrane proteins between the trans-Golgi network and the prevacuolar compartment. While several transcript variants may exist for this gene, the full-length natures of only two have been described to date. These two represent the major variants of this gene and encode distinct isoforms. [provided by RefSeq, Jul 2008]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nVPS13D functions as a lipid transfer protein that mediates communication at membrane contact sites between the endoplasmic reticulum (ER) and other organelles. In metazoans, VPS13D is recruited by mitochondrial-associated proteins (such as Miro) and, in a VAP‐dependent manner, forms a potential conduit for lipid exchange between the ER and mitochondria. Moreover, VPS13D has been implicated in the intracellular trafficking of membrane proteins between the trans‐Golgi network and the prevacuolar compartment, suggesting its broader role in maintaining membrane dynamics."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn addition to its role in establishing organelle communication, VPS13D coordinates lipid remodeling processes vital for energy metabolism. For example, it collaborates with components of the endosomal sorting complex, such as TSG101, to remodel lipid droplet membranes and thereby facilitate the transfer of fatty acids from lipid droplets to mitochondria."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nVPS13D is also essential for sustaining mitochondrial and peroxisomal integrity. Loss of VPS13D disrupts normal mitochondrial morphology, impairs peroxisome biogenesis, and interferes with autophagic clearance of damaged mitochondria. It further modulates mitochondrial dynamics by acting upstream of fusion regulators like Marf/Mfn2 and by negatively regulating excessive ER–mitochondria tethering through interactions with factors such as VCP/p97."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "4", "end_ref": "6"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nBeyond its roles in lipid and organelle homeostasis, VPS13D participates in the regulation of receptor trafficking. Notably, it interacts with the long non‐coding RNA SNHG1 to promote the membrane localization of the interleukin‑7 receptor, which in turn influences IL‑7 signaling and the transcriptional program underlying memory CD8 T cell differentiation."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "7"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nThe functional relevance of VPS13D is further underscored by disease studies. Mutations in VPS13D are associated with a spectrum of neurological and movement disorders—including spastic ataxia, spastic paraplegia, and complex hyperkinetic syndromes—which likely arise from the cumulative defects in lipid transport, impaired mitochondrial clearance, and disrupted organelle interactions. Yeast models have demonstrated that alterations in the conserved adaptor-binding (VAB) domain of VPS13D impede membrane recruitment, reinforcing its critical function in intracellular lipid trafficking."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "8", "end_ref": "10"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nAdditional studies have established a central role for VPS13D in maintaining mitochondrial homeostasis, thereby linking its dysfunction to neurodegenerative phenotypes. Indeed, recent reviews have emphasized that perturbations in VPS13D‐mediated lipid transfer and organelle contact may ultimately compromise cellular bioenergetics and contribute to disease pathogenesis."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "11"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Andrés Guillén-Samander, Marianna Leonzino, Michael G Hanna, et al. "}, {"type": "b", "children": [{"type": "t", "text": "VPS13D bridges the ER to mitochondria and peroxisomes via Miro."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Biol (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1083/jcb.202010004"}], "href": "https://doi.org/10.1083/jcb.202010004"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "33891013"}], "href": "https://pubmed.ncbi.nlm.nih.gov/33891013"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Hussein Algahtani, Bader Shirah, Muhammad Imran Naseer "}, {"type": "b", "children": [{"type": "t", "text": "Autosomal recessive spinocerebellar ataxia type 4 due to a novel homozygous mutation in the VPS13D gene in a Saudi family."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Clin Neurol Neurosurg (2024)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.clineuro.2024.108271"}], "href": "https://doi.org/10.1016/j.clineuro.2024.108271"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "38569247"}], "href": "https://pubmed.ncbi.nlm.nih.gov/38569247"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Jingru Wang, Na Fang, Juan Xiong, et al. "}, {"type": "b", "children": [{"type": "t", "text": "An ESCRT-dependent step in fatty acid transfer from lipid droplets to mitochondria through VPS13D-TSG101 interactions."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Commun (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41467-021-21525-5"}], "href": "https://doi.org/10.1038/s41467-021-21525-5"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "33623047"}], "href": "https://pubmed.ncbi.nlm.nih.gov/33623047"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Heather A Baldwin, Chunxin Wang, Gil Kanfer, et al. "}, {"type": "b", "children": [{"type": "t", "text": "VPS13D promotes peroxisome biogenesis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Biol (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1083/jcb.202001188"}], "href": "https://doi.org/10.1083/jcb.202001188"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "33891012"}], "href": "https://pubmed.ncbi.nlm.nih.gov/33891012"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "James L Shen, Tina M Fortier, Yan G Zhao, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Vmp1, Vps13D, and Marf/Mfn2 function in a conserved pathway to regulate mitochondria and ER contact in development and disease."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Curr Biol (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.cub.2021.04.062"}], "href": "https://doi.org/10.1016/j.cub.2021.04.062"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "34019822"}], "href": "https://pubmed.ncbi.nlm.nih.gov/34019822"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Yuanjiao Du, Jingru Wang, Juan Xiong, et al. "}, {"type": "b", "children": [{"type": "t", "text": "VPS13D interacts with VCP/p97 and negatively regulates endoplasmic reticulum-mitochondria interactions."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Biol Cell (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1091/mbc.E21-03-0097"}], "href": "https://doi.org/10.1091/mbc.E21-03-0097"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "34133214"}], "href": "https://pubmed.ncbi.nlm.nih.gov/34133214"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Yanyan Zhang, Baohua Li, Qiang Bai, et al. "}, {"type": "b", "children": [{"type": "t", "text": "The lncRNA Snhg1-Vps13D vesicle trafficking system promotes memory CD8 T cell establishment via regulating the dual effects of IL-7 signaling."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Signal Transduct Target Ther (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41392-021-00492-9"}], "href": "https://doi.org/10.1038/s41392-021-00492-9"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "33758164"}], "href": "https://pubmed.ncbi.nlm.nih.gov/33758164"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Julie Gauthier, Inge A Meijer, Davor Lessel, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Recessive mutations in VPS13D cause childhood onset movement disorders."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Ann Neurol (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/ana.25204"}], "href": "https://doi.org/10.1002/ana.25204"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "29518281"}], "href": "https://pubmed.ncbi.nlm.nih.gov/29518281"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Samantha K Dziurdzik, Björn D M Bean, Michael Davey, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A VPS13D spastic ataxia mutation disrupts the conserved adaptor-binding site in yeast Vps13."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Hum Mol Genet (2020)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/hmg/ddz318"}], "href": "https://doi.org/10.1093/hmg/ddz318"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31943017"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31943017"}]}, {"type": "r", "ref": 10, "children": [{"type": "t", "text": "Martje G Pauly, Norbert Brüggemann, Stephanie Efthymiou, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Not to Miss: Intronic Variants, Treatment, and Review of the Phenotypic Spectrum in "}, {"type": "a", "children": [{"type": "t", "text": "i"}], "href": "i"}, {"type": "t", "text": "VPS13D"}, {"type": "a", "children": [{"type": "t", "text": "/i"}], "href": "/i"}, {"type": "t", "text": "-Related Disorder."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Int J Mol Sci (2023)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.3390/ijms24031874"}], "href": "https://doi.org/10.3390/ijms24031874"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "36768210"}], "href": "https://pubmed.ncbi.nlm.nih.gov/36768210"}]}, {"type": "r", "ref": 11, "children": [{"type": "t", "text": "Tipu Sultan, Giovanna Scorrano, Marta Panciroli, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Clinical and molecular heterogeneity of VPS13D-related neurodevelopmental and movement disorders."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Gene (2024)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.gene.2023.148119"}], "href": "https://doi.org/10.1016/j.gene.2023.148119"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "38160741"}], "href": "https://pubmed.ncbi.nlm.nih.gov/38160741"}]}]}]}
Proteins	VP13D_HUMAN
NCBI Gene ID	55187
API
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Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

VPS13D has 6,438 functional associations with biological entities spanning 8 categories (molecular profile, organism, chemical, disease, phenotype or trait, functional term, phrase or reference, structural feature, cell line, cell type or tissue, gene, protein or microRNA) extracted from 115 datasets.

Click the + buttons to view associations for VPS13D from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

VPS13D Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Achilles Cell Line Gene Essentiality Profiles	cell lines with fitness changed by VPS13D gene knockdown relative to other cell lines from the Achilles Cell Line Gene Essentiality Profiles dataset.
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of VPS13D gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of VPS13D gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of VPS13D gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of VPS13D gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of VPS13D gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of VPS13D gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of VPS13D gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of VPS13D gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	Carcinogenome Chemical Perturbation Carcinogenicity Signatures	small molecule perturbations changing expression of VPS13D gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of VPS13D gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of VPS13D gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with VPS13D protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with VPS13D gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of VPS13D gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of VPS13D gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of VPS13D gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	ClinVar Gene-Phenotype Associations 2025	phenotypes associated with VPS13D gene from the curated ClinVar Gene-Phenotype Associations 2025 dataset.
	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	gene perturbations changing expression of VPS13D gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset.
	CM4AI U2OS Cell Map Protein Localization Assemblies	assemblies containing VPS13D protein from integrated AP-MS and IF data from the CM4AI U2OS Cell Map Protein Localization Assemblies dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of VPS13D gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing VPS13D protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing VPS13D protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with VPS13D protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with VPS13D protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with VPS13D gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with VPS13D gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with VPS13D gene/protein from the curated CTD Gene-Disease Associations dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of VPS13D protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
	DGIdb Drug Targets 2026	interacting drugs for VPS13D protein from the DGIdb Drug Targets 2026 dataset.
	DISEASES Curated Gene-Disease Association Evidence Scores 2025	diseases involving VPS13D gene from the DISEASES Curated Gene-Disease Association Evidence Scores 2025 dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with VPS13D gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with VPS13D gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with VPS13D gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with VPS13D gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with VPS13D gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at VPS13D 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 VPS13D gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of VPS13D gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing VPS13D from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.