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

Gene ID: 55187, updated on 27-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
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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
  • 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. Autosomal recessive spinocerebellar ataxia type 4 due to a novel homozygous mutation in the VPS13D gene in a Saudi family. Algahtani H, et al. Clin Neurol Neurosurg, 2024 May. PMID 38569247
  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 (62) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Clinical, genetic, and neuroimaging profiles of autosomal recessive spinocerebellar ataxia type 4 caused by novel VPS13D variants in Chinese.
    Title: Clinical, genetic, and neuroimaging profiles of autosomal recessive spinocerebellar ataxia type 4 caused by novel VPS13D variants in Chinese.
  2. 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.
  3. Clinical and molecular heterogeneity of VPS13D-related neurodevelopmental and movement disorders.
    Title: Clinical and molecular heterogeneity of VPS13D-related neurodevelopmental and movement disorders.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. VPS13D bridges the ER to mitochondria and peroxisomes via Miro.
    Title: VPS13D bridges the ER to mitochondria and peroxisomes via Miro.
  10. VPS13D promotes peroxisome biogenesis.
    Title: VPS13D promotes peroxisome biogenesis.
Submit: New GeneRIF Correction See all GeneRIFs (20)

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)

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

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