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VPS72 vacuolar protein sorting 72 homolog [ Homo sapiens (human) ]

Gene ID: 6944, updated on 5-Mar-2024

Summary

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Official Symbol
VPS72provided by HGNC
Official Full Name
vacuolar protein sorting 72 homologprovided by HGNC
Primary source
HGNC:HGNC:11644
See related
Ensembl:ENSG00000163159 MIM:600607; AllianceGenome:HGNC:11644
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
YL1; CFL1; Swc2; YL-1; TCFL1
Summary
The protein encoded by this gene is a shared subunit of two multi-component complexes, the histone acetyltransferase complex TRRAP/TIP60 as well as the chromatin remodeling SRCAP-containing complex. The TRRAP/TIP60 complex acetylates nucleosomal histones important for transcriptional regulation, double strand DNA break repair and apoptosis. The SRCAP-containing complex catalyzes the exchange of histone H2A with the histone variant Htz1 (H2AFZ) into nucleosomes. This protein may be responsible for binding H2AFZ, which has a role in chromosome segregation. This protein may also have a role in regulating long-term hematopoietic stem cell activity. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Aug 2012]
Expression
Ubiquitous expression in brain (RPKM 14.7), prostate (RPKM 14.0) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
1q21.3
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (151176304..151190197, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (150300033..150313938, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (151148780..151162673, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene TNFAIP8L2-SCNM1 readthrough Neighboring gene LysM domain containing 1 Neighboring gene TNF alpha induced protein 8 like 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:151137860-151138565 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151138566-151139272 Neighboring gene sodium channel modifier 1 Neighboring gene tropomodulin 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1711 Neighboring gene uncharacterized LOC124904419 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1712 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1713 Neighboring gene phosphatidylinositol-4-phosphate 5-kinase type 1 alpha Neighboring gene ReSE screen-validated silencer GRCh37_chr1:151183035-151183192 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:151183741-151184733 Neighboring gene MPRA-validated peak410 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1714 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1316 Neighboring gene Sharpr-MPRA regulatory region 10214 Neighboring gene proteasome 26S subunit ubiquitin receptor, non-ATPase 4

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. Forced expression of YL-1 protein suppresses the anchorage-independent growth of Kirsten sarcoma virus-transformed NIH3T3 cells. Horikawa I, et al. Exp Cell Res, 1995 Sep. PMID 7664828
  2. Vacuolar protein sorting-associated protein 72 homolog (VPS72) binding to lysine acetyltransferase 5 (KAT5) promotes the proliferation, invasion and migration of hepatocellular carcinoma through regulating phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) signaling pathway. Chen T, et al. Bioengineered, 2022 Apr. PMID 35383533, Free PMC Article
  3. VPS72/YL1-Mediated H2A.Z Deposition Is Required for Nuclear Reassembly after Mitosis. Moreno-Andrés D, et al. Cells, 2020 Jul 16. PMID 32708675, Free PMC Article
  4. Integrin-αvβ3 regulates thrombopoietin-mediated maintenance of hematopoietic stem cells. Umemoto T, et al. Blood, 2012 Jan 5. PMID 22096247, Free PMC Article
  5. Molecular cloning of a novel human cDNA on chromosome 1q21 and its mouse homolog encoding a nuclear protein with DNA-binding ability. Horikawa I, et al. Biochem Biophys Res Commun, 1995 Mar 28. PMID 7702631

See all (57) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Targeting VPS72 inhibits ACTL6A/MYC axis activity in HCC progression.
    Title: Targeting VPS72 inhibits ACTL6A/MYC axis activity in HCC progression.
  2. Vacuolar protein sorting-associated protein 72 homolog (VPS72) binding to lysine acetyltransferase 5 (KAT5) promotes the proliferation, invasion and migration of hepatocellular carcinoma through regulating phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) signaling pathway.
    Title: Vacuolar protein sorting-associated protein 72 homolog (VPS72) binding to lysine acetyltransferase 5 (KAT5) promotes the proliferation, invasion and migration of hepatocellular carcinoma through regulating phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT) signaling pathway.
  3. VPS72/YL1-Mediated H2A.Z Deposition Is Required for Nuclear Reassembly after Mitosis.
    Title: VPS72/YL1-Mediated H2A.Z Deposition Is Required for Nuclear Reassembly after Mitosis.
  4. The 2.7-A-resolution crystal structure of the human YL1-H2A.Z-H2B complex shows that YL1 binding, similarly to ANP32E binding, triggers an extension of the H2A.Z alphaC helix.
    Title: Molecular basis and specificity of H2A.Z-H2B recognition and deposition by the histone chaperone YL1.
  5. Results identify YL1 as a subunit of the TRRAP/TIP60 HAT complex, and also as a component of a novel mammalian multiprotein complex that includes the SNF2-related helicase SRCAP.
    Title: The mammalian YL1 protein is a shared subunit of the TRRAP/TIP60 histone acetyltransferase and SRCAP complexes.
Submit: New GeneRIF Correction

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP-dependent H2AZ histone chaperone activity IEA
Inferred from Electronic Annotation
more info
  
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables histone binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables histone chaperone activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in chromatin remodeling NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 PubMed 
involved_in positive regulation of DNA-templated transcription NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in positive regulation of double-strand break repair via homologous recombination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of DNA-templated transcription NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of apoptotic process NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of cell cycle IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of double-strand break repair NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in somatic stem cell population maintenance IEA
Inferred from Electronic Annotation
more info
  
involved_in transcription initiation-coupled chromatin remodeling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of NuA4 histone acetyltransferase complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear speck IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
part_of nucleosome IDA
Inferred from Direct Assay
more info
 PubMed 
part_of nucleosome NAS
Non-traceable Author Statement
more info
 PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
vacuolar protein sorting-associated protein 72 homolog
Names
transcription factor-like 1
transformation suppressor gene YL-1

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.

mRNA and Protein(s)

  1. NM_001271087.2 → NP_001258016.1  vacuolar protein sorting-associated protein 72 homolog isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AA128103, AW194498, BU539181, CX163016, DQ655941
    Consensus CDS
    CCDS59201.1
    UniProtKB/Swiss-Prot
    Q15906
    Related
    ENSP00000346464.4, ENST00000354473.4
    Conserved Domains (3) summary
    pfam04180
    Location:22 → 78
    LTV; Low temperature viability protein
    pfam05764
    Location:6 → 216
    YL1; YL1 nuclear protein
    pfam08265
    Location:302 → 330
    YL1_C; YL1 nuclear protein C-terminal domain

  2. NM_001271088.2 → NP_001258017.1  vacuolar protein sorting-associated protein 72 homolog isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses two alternate splice sites in the 3' coding region that result in a frameshift, compared to variant 1. The resulting protein (isoform 3) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AL592424, CT003766, DQ655941
    UniProtKB/TrEMBL
    B4DMP5
    Conserved Domains (1) summary
    pfam05764
    Location:7 → 193
    YL1; YL1 nuclear protein

  3. NM_005997.3 → NP_005988.1  vacuolar protein sorting-associated protein 72 homolog isoform 2

    See identical proteins and their annotated locations for NP_005988.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AA128103, AW194498, D43642, DQ655941
    Consensus CDS
    CCDS989.1
    UniProtKB/Swiss-Prot
    A6NLK9, A6PW55, Q15906, Q53GJ2, Q5U0R4
    Related
    ENSP00000357887.5, ENST00000368892.9
    Conserved Domains (3) summary
    pfam04180
    Location:22 → 78
    LTV; Low temperature viability protein
    pfam05764
    Location:6 → 216
    YL1; YL1 nuclear protein
    pfam08265
    Location:291 → 319
    YL1_C; YL1 nuclear protein C-terminal domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    151176304..151190197 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017002205.2 → XP_016857694.1  vacuolar protein sorting-associated protein 72 homolog isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    150300033..150313938 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054338527.1 → XP_054194502.1  vacuolar protein sorting-associated protein 72 homolog isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q15906.1 GenPept UniProtKB/Swiss-Prot:Q15906

Gene LinkOut

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