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    VPS13D vacuolar protein sorting 13 homolog D [ Homo sapiens (human) ]

    Gene ID: 55187, updated on 2-Nov-2024

    Summary

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    Official Symbol
    VPS13Dprovided by HGNC
    Official Full Name
    vacuolar protein sorting 13 homolog Dprovided by HGNC
    Primary source
    HGNC:HGNC:23595
    See related
    Ensembl:ENSG00000048707 MIM:608877; AllianceGenome:HGNC:23595
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SCA24; SCAR4; SCASI; BLTP5D
    Summary
    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]
    Expression
    Ubiquitous expression in skin (RPKM 12.9), thyroid (RPKM 9.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See VPS13D in Genome Data Viewer
    Location:
    1p36.22-p36.21
    Exon count:
    70
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (12230030..12512047)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (11774166..12056190)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (12290087..12572099)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900427 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:12289836-12290766 Neighboring gene ribosomal protein L10 pseudogene 17 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:12309525-12310516 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 212 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 213 Neighboring gene uncharacterized LOC124903845 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:12418393-12418894 Neighboring gene Sharpr-MPRA regulatory region 10571 Neighboring gene uncharacterized LOC124904680 Neighboring gene NFE2L2 motif-containing MPRA enhancer 265 Neighboring gene Sharpr-MPRA regulatory region 15009 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:12537802-12538659 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:12538660-12539516 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:12541249-12541767 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:12557015-12557515 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:12568463-12568964 Neighboring gene small nucleolar RNA, H/ACA box 59A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:12600378-12601026 Neighboring gene long intergenic non-protein coding RNA 2766 Neighboring gene Sharpr-MPRA regulatory region 4366 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:12608056-12608563 Neighboring gene Sharpr-MPRA regulatory region 1458 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:12612066-12613020 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:12613021-12613973 Neighboring gene RNA, U6atac small nuclear 18, pseudogene Neighboring gene dehydrogenase/reductase 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Clinical and molecular heterogeneity of VPS13D-related neurodevelopmental and movement disorders. Sultan T, et al. Gene, 2024 Mar 20. PMID 38160741
    2. Recessive mutations in VPS13D cause childhood onset movement disorders. Gauthier J, et al. Ann Neurol, 2018 Jun. PMID 29518281
    3. VPS13D Movement Disorder. Adam MP, et al. , 1993. PMID 30789691
    4. VPS13D Gene Variant Is Associated with Altered IL-6 Production and Mortality in Septic Shock. Nakada TA, et al. J Innate Immun, 2015. PMID 25896417, Free PMC Article
    5. VPS13D-related disorders presenting as a pure and complicated form of hereditary spastic paraplegia. Koh K, et al. Mol Genet Genomic Med, 2020 Mar. PMID 31876103, Free PMC Article

    See all (61) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Autosomal recessive spinocerebellar ataxia type 4 due to a novel homozygous mutation in the VPS13D gene in a Saudi family.
      Title: Autosomal recessive spinocerebellar ataxia type 4 due to a novel homozygous mutation in the VPS13D gene in a Saudi family.
    2. Clinical and molecular heterogeneity of VPS13D-related neurodevelopmental and movement disorders.
      Title: Clinical and molecular heterogeneity of VPS13D-related neurodevelopmental and movement disorders.
    3. Screening of candidate genes at GLC3B and GLC3C loci in Chinese primary congenital glaucoma patients with targeted next generation sequencing.
      Title: Screening of candidate genes at GLC3B and GLC3C loci in Chinese primary congenital glaucoma patients with targeted next generation sequencing.
    4. Not to Miss: Intronic Variants, Treatment, and Review of the Phenotypic Spectrum in VPS13D-Related Disorder.
      Title: Not to Miss: Intronic Variants, Treatment, and Review of the Phenotypic Spectrum in VPS13D-Related Disorder.
    5. VPS13D-based disease: Expansion of the clinical phenotype in two brothers and mutation diversity in the Turkish population.
      Title: VPS13D-based disease: Expansion of the clinical phenotype in two brothers and mutation diversity in the Turkish population.
    6. Vmp1, Vps13D, and Marf/Mfn2 function in a conserved pathway to regulate mitochondria and ER contact in development and disease.
      Title: Vmp1, Vps13D, and Marf/Mfn2 function in a conserved pathway to regulate mitochondria and ER contact in development and disease.
    7. VPS13D interacts with VCP/p97 and negatively regulates endoplasmic reticulum-mitochondria interactions.
      Title: VPS13D interacts with VCP/p97 and negatively regulates endoplasmic reticulum-mitochondria interactions.
    8. VPS13D bridges the ER to mitochondria and peroxisomes via Miro.
      Title: VPS13D bridges the ER to mitochondria and peroxisomes via Miro.
    9. VPS13D promotes peroxisome biogenesis.
      Title: VPS13D promotes peroxisome biogenesis.
    10. Genetic heterogeneity in Leigh syndrome: Highlighting treatable and novel genetic causes.
      Title: Genetic heterogeneity in Leigh syndrome: Highlighting treatable and novel genetic causes.
    Submit: New GeneRIF Correction See all GeneRIFs (19)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ23066

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in lipid transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mitochondrion organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitochondrion organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of mitophagy IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein retention in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein targeting to vacuole IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    located_in mitochondrion HTP PubMed 

    General protein information

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    Preferred Names
    intermembrane lipid transfer protein VPS13D
    Names
    bridge-like lipid transfer protein family member 5D
    spinocerebellar ataxia 24 (with saccadic intrusions)
    spinocerebellar ataxia with saccadic intrusions
    vacuolar protein sorting 13D
    vacuolar protein sorting-associated protein 13D

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_056877.1 RefSeqGene

      Range
      4992..287009
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1213

    mRNA and Protein(s)

    1. NM_015378.4 → NP_056193.2  intermembrane lipid transfer protein VPS13D isoform 1

      See identical proteins and their annotated locations for NP_056193.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AJ608774, AL031276, BC051804, BX682532, HY121734
      Consensus CDS
      CCDS30588.1
      UniProtKB/Swiss-Prot
      J3KP14, Q58F10, Q5THJ4, Q6MZK9, Q6ZV12, Q709C4, Q709C5, Q86UB4, Q9NSJ3, Q9UIM0
      Related
      ENSP00000478104.1, ENST00000620676.6
      Conserved Domains (6) summary
      cd14306
      Location:2642 → 2677
      UBA_VP13D; UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins
      pfam06650
      Location:3276 → 3559
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam12624
      Location:3 → 112
      Chorein_N; N-terminal region of Chorein or VPS13
      pfam16908
      Location:139 → 356
      VPS13; Vacuolar sorting-associated protein 13, N-terminal
      pfam16909
      Location:3984 → 4129
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
      pfam16910
      Location:614 → 894
      VPS13_mid_rpt; Repeating coiled region of VPS13

    2. NM_018156.4 → NP_060626.2  intermembrane lipid transfer protein VPS13D isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1
      Source sequence(s)
      AJ608775, AL031276, BC051804, BX682532, HY121734
      Consensus CDS
      CCDS30589.1
      UniProtKB/Swiss-Prot
      Q5THJ4
      Related
      ENSP00000482233.1, ENST00000613099.4
      Conserved Domains (6) summary
      cd14306
      Location:2642 → 2677
      UBA_VP13D; UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins
      pfam06650
      Location:3251 → 3534
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam12624
      Location:3 → 112
      Chorein_N; N-terminal region of Chorein or VPS13
      pfam16908
      Location:139 → 356
      VPS13; Vacuolar sorting-associated protein 13, N-terminal
      pfam16909
      Location:3959 → 4104
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
      pfam16910
      Location:614 → 894
      VPS13_mid_rpt; Repeating coiled region of VPS13

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      12230030..12512047
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      11774166..12056190
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5THJ4.2 GenPept UniProtKB/Swiss-Prot:Q5THJ4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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