VAC14 VAC14 component of PIKFYVE complex [Homo sapiens (human)] - Gene

Summary

Official Symbol: VAC14provided by HGNC
Official Full Name: VAC14 component of PIKFYVE complexprovided by HGNC
Primary source: HGNC:HGNC:25507
See related: Ensembl:ENSG00000103043 MIM:604632; AllianceGenome:HGNC:25507
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: TRX; TAX1BP2; ArPIKfyve
Summary: This gene encodes a scaffold protein that is a component of the PIKfyve protein kinase complex. This complex is responsible for the synthesis of phosphatidylinositol 3,5-bisphosphate, an important component of cellular membranes, from phosphatidylinositol 3-phosphate. Mice lacking a functional copy of this gene exhibit severe neurodegeneration. Mutations in the human gene have been identified in patients with a childhood onset progressive neurological disorder characterized by impaired movement, dystonia, and striatal abnormalities. [provided by RefSeq, May 2017]
Expression: Ubiquitous expression in lymph node (RPKM 2.8), thyroid (RPKM 2.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16q22.1-q22.2

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (70687439..70801158, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (76498610..76612330, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (70721342..70835061, complement)

Chromosome 16 - NC_000016.10 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
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?

TIG1 Inhibits the mTOR Signaling Pathway in Malignant Melanoma Through the VAC14 Protein.
Title: TIG1 Inhibits the mTOR Signaling Pathway in Malignant Melanoma Through the VAC14 Protein.
Proximity Interactome Map of the Vac14-Fig4 Complex Using BioID.
Title: Proximity Interactome Map of the Vac14-Fig4 Complex Using BioID.
Altered homodimer formation and increased iron accumulation in VAC14-related disease: Case report and review of the literature.
Title: Altered homodimer formation and increased iron accumulation in VAC14-related disease: Case report and review of the literature.
Novel VAC14 variants identified in two Chinese siblings with childhood-onset striatonigral degeneration.
Title: Novel VAC14 variants identified in two Chinese siblings with childhood-onset striatonigral degeneration.
The patient fibroblasts showed extensive vacuolization, characteristic of VAC14-related disorders.
Title: Homozygous variant, p.(Arg643Trp) in VAC14 causes striatonigral degeneration: report of a novel variant and review of VAC14-related disorders.
Increased albuminuria in Vac14(L156R)-overexpressing mice is a consequence of a lowered endo- and transcytosis of albumin in renal tubules.
Title: Nephron-specific knockin of the PIKfyve-binding-deficient Vac14(L156R) mutant results in albuminuria and mesangial expansion.
Nbeal2 interacts with Dock7, Sec16a, and Vac14.
Title: Nbeal2 interacts with Dock7, Sec16a, and Vac14.
The association data demonstrated strong correlations between rs8060947 and VAC14 expression and between rs8060947 and S. Typhi invasion. The direction of effects for the different alleles led to the hypothesis that reducing VAC14 expression would increase S. Typhi invasion.
Title: Human genetic variation in VAC14 regulates Salmonella invasion and typhoid fever through modulation of cholesterol.
A genome-wide association study of a prospectively enrolled patient cohort identified an single nucleotide polymorphism in VAC14 that predicts sensitivity to docetaxel-induced peripheral neuropathy.
Title: Pharmacogenetic Discovery in CALGB (Alliance) 90401 and Mechanistic Validation of a VAC14 Polymorphism that Increases Risk of Docetaxel-Induced Neuropathy.
Biallelic rare coding variants in VAC14 was identified in a female neonate with Yunis-Varon syndrome. Cultured patient fibroblasts exhibited a YVS-like vacuolation ameliorated by ML-SA1.
Title: Yunis-Varón syndrome caused by biallelic VAC14 mutations.

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

Associated conditions

Description	Tests
Striatonigral degeneration, childhood-onset MedGen: C4310743 OMIM: 617054 GeneReviews: Not available	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

D16S2796 (e-PCR)
- UniSTS:153366

STS-AA011691 (e-PCR)
- UniSTS:64552

D16S2659 (e-PCR)
- UniSTS:152398

SHGC-61090 (e-PCR)
- UniSTS:75631

D16S3397 (e-PCR)
- UniSTS:54704

SHGC-148340 (e-PCR)
- UniSTS:176334

G63042 (e-PCR)
- UniSTS:140017

STS-U25801 (e-PCR)
- UniSTS:69364

Clone Names

FLJ10305, FLJ36622, FLJ46582, MGC149815, MGC149816

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables signaling receptor activity	NAS Non-traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in phosphatidylinositol biosynthetic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of postsynaptic neurotransmitter receptor internalization	IEA Inferred from Electronic Annotation more info
involved_in signal transduction	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi membrane	TAS Traceable Author Statement more info
part_of PAS complex	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in early endosome membrane	TAS Traceable Author Statement more info
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
is_active_in endosome membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in late endosome membrane	TAS Traceable Author Statement more info
located_in presynaptic endosome	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: protein VAC14 homolog

Names: Vac14, PIKFYVE complex component

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_054902.1 RefSeqGene

Range

5012..118731

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001351157.2 → NP_001338086.1 protein VAC14 homolog isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1.

Source sequence(s)

AC020763, AC027281, AK307766, AL137396

Conserved Domains (1) summary

pfam11916
Location:308 → 483

Vac14_Fig4_bd; Vacuolar protein 14 C-terminal Fig4p binding
NM_018052.5 → NP_060522.3 protein VAC14 homolog isoform 1

See identical proteins and their annotated locations for NP_060522.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AK056433, AL137396

Consensus CDS

CCDS10896.1

UniProtKB/Swiss-Prot

B3KPJ5, B3KSM8, Q08AM6, Q13174, Q6IA12, Q7L4Y1, Q9BW96, Q9H6V6

UniProtKB/TrEMBL

B4DMP4

Related

ENSP00000261776.5, ENST00000261776.10

Conserved Domains (3) summary

sd00044
Location:94 → 122

HEAT; HEAT repeat [structural motif]

pfam11916
Location:542 → 717

Vac14_Fig4_bd; Vacuolar protein 14 C-terminal Fig4p binding

pfam12755
Location:67 → 163

Vac14_Fab1_bd; Vacuolar 14 Fab1-binding region

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

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

70687439..70801158 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005256038.5 → XP_005256095.1 protein VAC14 homolog isoform X1

UniProtKB/TrEMBL

B4DMP4

Conserved Domains (3) summary

pfam11916
Location:543 → 717

Vac14_Fig4_bd; Vacuolar protein 14 C-terminal Fig4p binding

pfam12755
Location:67 → 163

Vac14_Fab1_bd; Vacuolar 14 Fab1-binding region

sd00044
Location:94 → 122

HEAT; HEAT repeat [structural motif]
XM_011523225.4 → XP_011521527.1 protein VAC14 homolog isoform X2

Conserved Domains (2) summary

pfam12755
Location:67 → 163

Vac14_Fab1_bd; Vacuolar 14 Fab1-binding region

sd00044
Location:53 → 78

HEAT; HEAT repeat [structural motif]
XM_047434360.1 → XP_047290316.1 protein VAC14 homolog isoform X3

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

76498610..76612330 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054313459.1 → XP_054169434.1 protein VAC14 homolog isoform X1

UniProtKB/TrEMBL

B4DMP4
XM_054313460.1 → XP_054169435.1 protein VAC14 homolog isoform X2
XM_054313461.1 → XP_054169436.1 protein VAC14 homolog isoform X3