VPS13A vacuolar protein sorting 13 homolog A [Homo sapiens (human)] - Gene

Summary

Official Symbol: VPS13Aprovided by HGNC
Official Full Name: vacuolar protein sorting 13 homolog Aprovided by HGNC
Primary source: HGNC:HGNC:1908
See related: Ensembl:ENSG00000197969 MIM:605978; AllianceGenome:HGNC:1908
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: CHAC; BLTP5A; CHOREIN
Summary: 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]
Expression: Ubiquitous expression in testis (RPKM 7.5), skin (RPKM 6.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9q21.2

Exon count:: 74

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (77177534..77421537)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (89334100..89578104)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (79792450..80036453)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Clinical Features and Novel Pathogenic Variants of Chinese Patients With McLeod Syndrome and Chorea-Acanthocytosis.
Title: Clinical Features and Novel Pathogenic Variants of Chinese Patients With McLeod Syndrome and Chorea-Acanthocytosis.
An Autopsy Series of Seven Cases of VPS13A Disease (Chorea-Acanthocytosis).
Title: An Autopsy Series of Seven Cases of VPS13A Disease (Chorea-Acanthocytosis).
Chorein sensitive microtubule organization in tumor cells.
Title: Chorein sensitive microtubule organization in tumor cells.
Exome sequencing of choreoacanthocytosis reveals novel mutations in VPS13A and co-mutation in modifier gene(s).
Title: Exome sequencing of choreoacanthocytosis reveals novel mutations in VPS13A and co-mutation in modifier gene(s).
The association of lipid transfer protein VPS13A with endosomes is mediated by sorting nexin SNX5.
Title: The association of lipid transfer protein VPS13A with endosomes is mediated by sorting nexin SNX5.
Interaction between VPS13A and the XK scramblase is important for VPS13A function in humans.
Title: Interaction between VPS13A and the XK scramblase is important for VPS13A function in humans.
A partnership between the lipid scramblase XK and the lipid transfer protein VPS13A at the plasma membrane.
Title: A partnership between the lipid scramblase XK and the lipid transfer protein VPS13A at the plasma membrane.
Structural and biochemical insights into lipid transport by VPS13 proteins.
Title: Structural and biochemical insights into lipid transport by VPS13 proteins.
XK is a partner for VPS13A: a molecular link between Chorea-Acanthocytosis and McLeod Syndrome.
Title: XK is a partner for VPS13A: a molecular link between Chorea-Acanthocytosis and McLeod Syndrome.
Translational study of the whole transcriptome in rats and genetic polymorphisms in humans identifies LRP1B and VPS13A as key genes involved in tolerance to cocaine-induced motor disturbances.
Title: Translational study of the whole transcriptome in rats and genetic polymorphisms in humans identifies LRP1B and VPS13A as key genes involved in tolerance to cocaine-induced motor disturbances.

Submit: New GeneRIF Correction See all GeneRIFs (39)

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

Associated conditions

Description	Tests
Chorea-acanthocytosis MedGen: C0393576 OMIM: 200150 GeneReviews: VPS13A Disease	Compare labs

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

D9S1674 (e-PCR), detects polymorphism
- UniSTS:53043

D9S1768 (e-PCR)
- UniSTS:15488

SHGC-150824 (e-PCR)
- UniSTS:173196

AB055267 (e-PCR)
- UniSTS:480145

D9S2082 (e-PCR)
- UniSTS:40343

SHGC-32427 (e-PCR)
- UniSTS:77535

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in Golgi to endosome transport	NAS Non-traceable Author Statement more info	PubMed
involved_in adult locomotory behavior	IEA Inferred from Electronic Annotation more info
involved_in autophagy	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within autophagy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in brain-derived neurotrophic factor receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in cellular response to osmotic stress	IEA Inferred from Electronic Annotation more info
involved_in erythrocyte differentiation	IEA Inferred from Electronic Annotation more info
involved_in exploration behavior	IEA Inferred from Electronic Annotation more info
involved_in flagellated sperm motility	IEA Inferred from Electronic Annotation more info
involved_in gene expression	IEA Inferred from Electronic Annotation more info
involved_in lipid transport	IEA Inferred from Electronic Annotation more info
involved_in long-term synaptic depression	IEA Inferred from Electronic Annotation more info
involved_in lysosomal protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in microglia differentiation	IEA Inferred from Electronic Annotation more info
involved_in motor behavior	IEA Inferred from Electronic Annotation more info
involved_in multicellular organism growth	IEA Inferred from Electronic Annotation more info
involved_in neuroinflammatory response	IEA Inferred from Electronic Annotation more info
involved_in neuromuscular process controlling balance	IEA Inferred from Electronic Annotation more info
involved_in neuron projection arborization	IEA Inferred from Electronic Annotation more info
involved_in protein localization	NAS Non-traceable Author Statement more info	PubMed
involved_in protein retention in Golgi apparatus	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein secretion	IEA Inferred from Electronic Annotation more info
involved_in protein targeting to vacuole	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to environmental enrichment	IEA Inferred from Electronic Annotation more info
involved_in social behavior	IEA Inferred from Electronic Annotation more info
involved_in sperm mitochondrion organization	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum membrane	IDA Inferred from Direct Assay more info	PubMed
located_in endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in lipid droplet	IDA Inferred from Direct Assay more info	PubMed
located_in lysosomal membrane	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondria-associated endoplasmic reticulum membrane contact site	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrial membrane	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrial outer membrane	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrion	HTP more info	PubMed
located_in neuron projection	IEA Inferred from Electronic Annotation more info
located_in neuronal cell body	IEA Inferred from Electronic Annotation more info
located_in neuronal dense core vesicle lumen	ISS Inferred from Sequence or Structural Similarity more info
located_in sperm midpiece	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: intermembrane lipid transfer protein VPS13A

Names: bridge-like lipid transfer protein family member 5A; chorea-acanthocytosis protein; vacuolar protein sorting 13A; vacuolar protein sorting-associated protein 13A

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

NG_008931.2 RefSeqGene

Range

5002..249005

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001018037.2 → NP_001018047.1 intermembrane lipid transfer protein VPS13A isoform C

See identical proteins and their annotated locations for NP_001018047.1

Status: REVIEWED

Description

Transcript Variant: This variant (C), also known as 2A, lacks an alternate in-frame segment, compared to variant A, resulting in a shorter protein (isoform C), compared to isoform A.

Source sequence(s)

AJ608769, AK027023, AL158159, AW303378

Consensus CDS

CCDS55321.1

Related

ENSP00000365823.3, ENST00000376636.7

Conserved Domains (7) summary

COG5043
Location:4 → 2065

MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]

pfam06650
Location:2170 → 2413

SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13

pfam09333
Location:2907 → 2986

ATG_C; Autophagy-related protein C terminal domain

pfam12624
Location:4 → 113

Chorein_N; N-terminal region of Chorein or VPS13

pfam16908
Location:142 → 371

VPS13; Vacuolar sorting-associated protein 13, N-terminal

pfam16909
Location:2727 → 2904

VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

pfam16910
Location:570 → 793

VPS13_mid_rpt; Repeating coiled region of VPS13
NM_001018038.3 → NP_001018048.1 intermembrane lipid transfer protein VPS13A isoform D

See identical proteins and their annotated locations for NP_001018048.1

Status: REVIEWED

Description

Transcript Variant: This variant (D), also known as 1D, contains a distinct 3' coding region and 3' UTR, compared to variant A. The resulting isoform (D) has a shorter C-terminus compared to isoform A.

Source sequence(s)

AJ626859, AK027023, AW303378, BF801459, BQ011213, CB104862, CN348731

Consensus CDS

CCDS47983.1

Related

ENSP00000496361.1, ENST00000645632.1

Conserved Domains (7) summary

COG5043
Location:4 → 2104

MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]

pfam06650
Location:2209 → 2452

SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13

pfam09333
Location:2946 → 3025

ATG_C; Autophagy-related protein C terminal domain

pfam12624
Location:4 → 113

Chorein_N; N-terminal region of Chorein or VPS13

pfam16908
Location:142 → 371

VPS13; Vacuolar sorting-associated protein 13, N-terminal

pfam16909
Location:2766 → 2943

VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

pfam16910
Location:570 → 793

VPS13_mid_rpt; Repeating coiled region of VPS13
NM_015186.4 → NP_056001.1 intermembrane lipid transfer protein VPS13A isoform B

See identical proteins and their annotated locations for NP_056001.1

Status: REVIEWED

Description

Transcript Variant: This variant (B) contains a distinct 3' coding region and 3' UTR, compared to variant A. The resulting isoform (B) has a shorter C-terminus compared to isoform A.

Source sequence(s)

AB054005, AK027023, EB387114

Consensus CDS

CCDS6656.1

Related

ENSP00000493592.1, ENST00000643348.1

Conserved Domains (7) summary

COG5043
Location:4 → 2104

MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]

pfam06650
Location:2209 → 2452

SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13

pfam09333
Location:2946 → 3025

ATG_C; Autophagy-related protein C terminal domain

pfam12624
Location:4 → 113

Chorein_N; N-terminal region of Chorein or VPS13

pfam16908
Location:142 → 371

VPS13; Vacuolar sorting-associated protein 13, N-terminal

pfam16909
Location:2766 → 2943

VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

pfam16910
Location:570 → 793

VPS13_mid_rpt; Repeating coiled region of VPS13
NM_033305.3 → NP_150648.2 intermembrane lipid transfer protein VPS13A isoform A

See identical proteins and their annotated locations for NP_150648.2

Status: REVIEWED

Description

Transcript Variant: This variant (A) encodes the longest isoform (A).

Source sequence(s)

AB054005, AF337532, AK027023, AL158159, AW303378

Consensus CDS

CCDS6655.1

UniProtKB/Swiss-Prot

Q5JSX9, Q5JSY0, Q5VYR5, Q702P4, Q709D0, Q86YF8, Q96RL7, Q96S61, Q9H995, Q9Y2J1

Related

ENSP00000353422.3, ENST00000360280.8

Conserved Domains (7) summary

COG5043
Location:4 → 2104

MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]

pfam06650
Location:2209 → 2452

SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13

pfam09333
Location:2946 → 3025

ATG_C; Autophagy-related protein C terminal domain

pfam12624
Location:4 → 113

Chorein_N; N-terminal region of Chorein or VPS13

pfam16908
Location:142 → 371

VPS13; Vacuolar sorting-associated protein 13, N-terminal

pfam16909
Location:2766 → 2943

VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

pfam16910
Location:570 → 793

VPS13_mid_rpt; Repeating coiled region of VPS13