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    ZFYVE28 zinc finger FYVE-type containing 28 [ Homo sapiens (human) ]

    Gene ID: 57732, updated on 17-Jun-2024

    Summary

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    Official Symbol
    ZFYVE28provided by HGNC
    Official Full Name
    zinc finger FYVE-type containing 28provided by HGNC
    Primary source
    HGNC:HGNC:29334
    See related
    Ensembl:ENSG00000159733 MIM:614176; AllianceGenome:HGNC:29334
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LST2; LYST2; lst-2
    Summary
    Enables phosphatidylinositol-3-phosphate binding activity. Involved in negative regulation of epidermal growth factor-activated receptor activity. Located in cytosol and early endosome membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in testis (RPKM 1.1), brain (RPKM 1.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZFYVE28 in Genome Data Viewer
    Location:
    4p16.3
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (2269597..2418645, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (2268369..2417399, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (2271324..2420372, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene DNA polymerase nu Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:2243031-2243532 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15158 Neighboring gene cytochrome c oxidase subunit 6B1 pseudogene 5 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:2258841-2258999 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2262363-2262955 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15159 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15161 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2264187-2264848 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2264849-2265508 Neighboring gene HAUS augmin like complex subunit 3 Neighboring gene CRISPRi-validated cis-regulatory element chr4.319 Neighboring gene microRNA 4800 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2282283-2282784 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2282785-2283284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2287193-2287694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2287695-2288194 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2290045-2290567 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15163 Neighboring gene MAX dimerization protein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15164 Neighboring gene Sharpr-MPRA regulatory region 1470 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2323631-2324130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2332641-2333140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2333455-2334252 Neighboring gene RNA, 7SL, cytoplasmic 589, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2334253-2335050 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2335051-2335848 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2335849-2336646 Neighboring gene uncharacterized LOC124900649 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2341140-2341829 Neighboring gene uncharacterized LOC105374352 Neighboring gene Spi-C transcription factor pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15165 Neighboring gene uncharacterized LOC107986249 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2388710-2389224 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2390450-2391184 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2391185-2391918 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2391919-2392652 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2392653-2393385 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:2395333-2395503 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21170 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21171 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2403273-2403944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2409813-2410318 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2413256-2413776 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2413777-2414297 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21173 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2417974-2418532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2418533-2419091 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15166 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15167 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2424482-2425072 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2425073-2425662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2425663-2426252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2426253-2426841 Neighboring gene cilia and flagella associated protein 99 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15169 Neighboring gene uncharacterized LOC105374353 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2465175-2465674 Neighboring gene uncharacterized LOC107986250

    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. FYVE domain-containing protein ZFYVE28 regulates EGFR-signaling in podocytes but is not critical for the function of filtration barrier in mice. Zambrano S, et al. Sci Rep, 2018 Mar 16. PMID 29549365, Free PMC Article
    2. Monoubiquitinylation regulates endosomal localization of Lst2, a negative regulator of EGF receptor signaling. Mosesson Y, et al. Dev Cell, 2009 May. PMID 19460345, Free PMC Article
    3. Genome-wide association study of clinical dimensions of schizophrenia: polygenic effect on disorganized symptoms. Fanous AH, et al. Am J Psychiatry, 2012 Dec. PMID 23212062, Free PMC Article
    4. Protein microarray analysis identifies human cellular prion protein interactors. Satoh J, et al. Neuropathol Appl Neurobiol, 2009 Feb. PMID 18482256
    5. Prediction of the coding sequences of unidentified human genes. XVIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 2000 Aug 31. PMID 10997877

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ZFYVE28 mediates insulin resistance by promoting phosphorylated insulin receptor degradation via increasing late endosomes production.
      Title: ZFYVE28 mediates insulin resistance by promoting phosphorylated insulin receptor degradation via increasing late endosomes production.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    3. Study concludes that endosomal localization of Lst2 (ZFYVE28), along with an ability to divert incoming EGFR molecules to degradation in lysosomes, is regulated by ubiquitinylation/deubiquitinylation cycles.
      Title: Monoubiquitinylation regulates endosomal localization of Lst2, a negative regulator of EGF receptor signaling.
    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

    EBI GWAS Catalog

    Description
    Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
    EBI GWAS Catalog
    Genome-wide association study of clinical dimensions of schizophrenia: polygenic effect on disorganized symptoms.
    EBI GWAS Catalog

    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

    Clone Names

    • MGC43699, MGC61592

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatidylinositol-3-phosphate binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of epidermal growth factor receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of epidermal growth factor-activated receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of epidermal growth factor-activated receptor activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in early endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in early endosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    lateral signaling target protein 2 homolog
    Names
    hLst2
    lateral signaling target-2 homolog
    zinc finger FYVE domain-containing protein 28
    zinc finger, FYVE domain containing 28

    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_001172656.2 → NP_001166127.1  lateral signaling target protein 2 homolog isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) represents use of an alternate promoter and 5' UTR, uses an upstream start codon, and lacks an alternate in-frame exon, compared to variant 1. The resulting isoform (3) has a longer N-terminus and lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AB046863, AK293775, AK294710, AL645924, BC032605, BC137309, BM128958
      Consensus CDS
      CCDS54711.1
      UniProtKB/Swiss-Prot
      Q9HCC9
      Related
      ENSP00000425706.1, ENST00000511071.5
      Conserved Domains (1) summary
      cd15731
      Location:780 → 844
      FYVE_LST2; FYVE domain found in lateral signaling target protein 2 homolog (Lst2) and similar proteins

    2. NM_001172657.2 → NP_001166128.1  lateral signaling target protein 2 homolog isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) represents use of an alternate promoter and 5' UTR, uses an upstream start codon, and uses an alternate 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (4) has a longer N-terminus and a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AL158068, AL645924, BC032605, BC053664
      Consensus CDS
      CCDS54712.1
      UniProtKB/Swiss-Prot
      Q9HCC9
      Related
      ENSP00000423694.1, ENST00000503000.1

    3. NM_001172658.3 → NP_001166129.1  lateral signaling target protein 2 homolog isoform 5

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) represents use of an alternate promoter and 5' UTR, uses an upstream start codon, and uses an alternate 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (5) has a longer N-terminus and a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AL645924, BC032605, BC035793, BC137310
      Consensus CDS
      CCDS54710.1
      UniProtKB/Swiss-Prot
      Q9HCC9
      Related
      ENSP00000422638.1, ENST00000509171.5

    4. NM_001172659.2 → NP_001166130.1  lateral signaling target protein 2 homolog isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes isoform 1.
      Source sequence(s)
      AB046863, AK294874, AK316484, BC035793, BC137310, BM128958
      Consensus CDS
      CCDS54708.1
      UniProtKB/Swiss-Prot
      Q9HCC9
      Related
      ENSP00000426299.1, ENST00000515312.5
      Conserved Domains (1) summary
      cd15731
      Location:740 → 804
      FYVE_LST2; FYVE domain found in lateral signaling target protein 2 homolog (Lst2) and similar proteins

    5. NM_001172660.3 → NP_001166131.1  lateral signaling target protein 2 homolog isoform 6

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) uses an alternate 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (6) has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AK316484, BC035793, BC137310
      Consensus CDS
      CCDS54709.1
      UniProtKB/Swiss-Prot
      Q9HCC9
      Related
      ENSP00000425766.1, ENST00000515169.5

    6. NM_020972.3 → NP_066023.2  lateral signaling target protein 2 homolog isoform 2

      See identical proteins and their annotated locations for NP_066023.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) represents use of an alternate promoter and 5' UTR and uses an upstream start codon, compared to variant 1. The resulting isoform (2) has a longer N-terminus, compared to isoform 1.
      Source sequence(s)
      AB046863, AK294874, AL645924, BC032605, BC137310, BM128958
      Consensus CDS
      CCDS33942.1
      UniProtKB/Swiss-Prot
      B2RP83, B3KX50, B7Z1Q7, B7Z2G9, B7Z2M2, B7ZB19, E9PB54, E9PB64, E9PG77, Q7Z6J3, Q9HCC9
      Related
      ENSP00000290974.3, ENST00000290974.7
      Conserved Domains (1) summary
      cd15731
      Location:810 → 874
      FYVE_LST2; FYVE domain found in lateral signaling target protein 2 homolog (Lst2) and similar proteins

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      2269597..2418645 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      2268369..2417399 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HCC9.3 GenPept UniProtKB/Swiss-Prot:Q9HCC9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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