Human Gene VPS13A (ENST00000376636.7) from GENCODE V44
  Description: Homo sapiens vacuolar protein sorting 13 homolog A (VPS13A), transcript variant C, mRNA. (from RefSeq NM_001018037)
RefSeq Summary (NM_001018037): The protein encoded by this gene may control steps in the cycling of proteins through the trans-Golgi network to endosomes, lysosomes and the plasma membrane. Mutations in this gene cause the autosomal recessive disorder, chorea-acanthocytosis. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000376636.7
Gencode Gene: ENSG00000197969.14
Transcript (Including UTRs)
   Position: hg38 chr9:77,177,445-77,417,483 Size: 240,039 Total Exon Count: 71 Strand: +
Coding Region
   Position: hg38 chr9:77,177,705-77,416,006 Size: 238,302 Coding Exon Count: 71 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:77,177,445-77,417,483)mRNA (may differ from genome)Protein (3135 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VP13A_HUMAN
DESCRIPTION: RecName: Full=Vacuolar protein sorting-associated protein 13A; AltName: Full=Chorea-acanthocytosis protein; AltName: Full=Chorein;
FUNCTION: May play a role in the control of protein cycling through the trans-Golgi network to early and late endosomes, lysosomes and plasma membrane.
INTERACTION: P16333:NCK1; NbExp=3; IntAct=EBI-1752583, EBI-389883;
TISSUE SPECIFICITY: Widely expressed. Higher expression is found in brain, heart, skeletal muscle and kidney.
DISEASE: Defects in VPS13A are the cause of chorea-acanthocytosis (CHAC) [MIM:200150]; also known as Levine-Critchley syndrome. CHAC is an autosomal recessive neurodegenerative disorder characterized by the gradual onset of hyperkinetic movements and abnormal erythrocyte morphology. Basal ganglia atrophy in the brain is a pathological feature of the disease. Other clinical symptoms include psychiatric features, epilepsy, peripheral neuropathy, myopathy and oral self-mutilation.
SIMILARITY: Belongs to the VPS13 family.
SIMILARITY: Contains 10 TPR repeats.
SEQUENCE CAUTION: Sequence=AAH20576.1; Type=Miscellaneous discrepancy; Note=Intron retention;
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/VPS13A";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: VPS13A
Diseases sorted by gene-association score: choreoacanthocytosis* (1721), curly hair-acral keratoderma-caries syndrome (22), lingual-facial-buccal dyskinesia (16), choreatic disease (9), neurodegeneration with brain iron accumulation (8), leukodystrophy, hypomyelinating, 2 (6), neurodegeneration with brain iron accumulation 6 (6), neurodegeneration with brain iron accumulation 1 (6), rem sleep behavior disorder (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D000082 Acetaminophen
  • C009618 O,O-diethyl O-3,5,6-trichloro-2-pyridyl phosphate
  • C006780 bisphenol A
  • C548651 2-(1'H-indolo-3'-carbonyl)thiazole-4-carboxylic acid methyl ester
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • D015127 9,10-Dimethyl-1,2-benzanthracene
  • D016604 Aflatoxin B1
  • D001564 Benzo(a)pyrene
  • D019256 Cadmium Chloride
  • D002117 Calcitriol
          more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 7.63 RPKM in Testis
Total median expression: 187.50 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -139.10260-0.535 Picture PostScript Text
3' UTR -308.901477-0.209 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR015412 - Autophagy-rel_C
IPR026847 - VPS13
IPR026854 - VPS13A_N
IPR009543 - VPSAP

Pfam Domains:
PF09333 - Autophagy-related protein C terminal domain
PF12624 - N-terminal region of Chorein or VPS13
PF06650 - SHR-binding domain of vacuolar-sorting associated protein 13

ModBase Predicted Comparative 3D Structure on Q96RL7
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0006895 Golgi to endosome transport
GO:0006914 autophagy
GO:0007399 nervous system development
GO:0007626 locomotory behavior
GO:0008104 protein localization
GO:0015031 protein transport
GO:0035176 social behavior

Cellular Component:
GO:0005622 intracellular
GO:0005829 cytosol
GO:0031045 dense core granule


-  Descriptions from all associated GenBank mRNAs
  AJ626859 - Homo sapiens mRNA for chorein 1D (VPS13A gene).
AF337532 - Homo sapiens chorea-acanthocytosis (CHAC) mRNA, complete cds.
AJ608769 - Homo sapiens mRNA for chorein 2A (CHAC) protein, transcript variant 2A (VPS13A gene).
AB054005 - Homo sapiens chac mRNA for chorein, complete cds.
BC172755 - Synthetic construct Homo sapiens clone IMAGE:9095600; MGC:199460 vacuolar protein sorting 13 homolog A (S. cerevisiae) (VPS13A) gene, encodes complete protein.
AB023203 - Homo sapiens mRNA for KIAA0986 protein, partial cds.
BC020576 - Homo sapiens vacuolar protein sorting 13 homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:3450315), partial cds.
BC041852 - Homo sapiens vacuolar protein sorting 13 homolog A (S. cerevisiae), mRNA (cDNA clone IMAGE:5270397), partial cds.
LF211271 - JP 2014500723-A/18774: Polycomb-Associated Non-Coding RNAs.
MA446848 - JP 2018138019-A/18774: Polycomb-Associated Non-Coding RNAs.
JD398052 - Sequence 379076 from Patent EP1572962.
JD108826 - Sequence 89850 from Patent EP1572962.
JD218281 - Sequence 199305 from Patent EP1572962.
JD404697 - Sequence 385721 from Patent EP1572962.
JD240080 - Sequence 221104 from Patent EP1572962.
JD144440 - Sequence 125464 from Patent EP1572962.
JD479785 - Sequence 460809 from Patent EP1572962.
LF345118 - JP 2014500723-A/152621: Polycomb-Associated Non-Coding RNAs.
MA580695 - JP 2018138019-A/152621: Polycomb-Associated Non-Coding RNAs.
AK124024 - Homo sapiens cDNA FLJ42030 fis, clone SPLEN2036953, highly similar to Vacuolar protein sorting 13A.
AK000273 - Homo sapiens cDNA FLJ20266 fis, clone HEP00615, highly similar to AB023203 Homo sapiens mRNA for KIAA0986 protein.
AK022967 - Homo sapiens cDNA FLJ12905 fis, clone NT2RP2004366, weakly similar to VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VPS13.
AK027023 - Homo sapiens cDNA: FLJ23370 fis, clone HEP15944.
JD026576 - Sequence 7600 from Patent EP1572962.
JD377236 - Sequence 358260 from Patent EP1572962.
JD042233 - Sequence 23257 from Patent EP1572962.
JD279798 - Sequence 260822 from Patent EP1572962.
JD416154 - Sequence 397178 from Patent EP1572962.
JD393840 - Sequence 374864 from Patent EP1572962.
JD044168 - Sequence 25192 from Patent EP1572962.
JD304715 - Sequence 285739 from Patent EP1572962.
JD145458 - Sequence 126482 from Patent EP1572962.
JD258249 - Sequence 239273 from Patent EP1572962.
JD043476 - Sequence 24500 from Patent EP1572962.
JD245257 - Sequence 226281 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: CHAC, ENST00000376636.1, ENST00000376636.2, ENST00000376636.3, ENST00000376636.4, ENST00000376636.5, ENST00000376636.6, KIAA0986, NM_001018037, Q5JSX9, Q5JSY0, Q5VYR5, Q702P4, Q709D0, Q86YF8, Q96RL7, Q96S61, Q9H995, Q9Y2J1, uc004aks.1, uc004aks.2, uc004aks.3, VP13A_HUMAN
UCSC ID: ENST00000376636.7
RefSeq Accession: NM_001018037
Protein: Q96RL7 (aka VP13A_HUMAN or V13A_HUMAN)
CCDS: CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene VPS13A:
chac (VPS13A Disease)
dystonia-ov (Hereditary Dystonia Overview)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.