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    LZTFL1 leucine zipper transcription factor like 1 [ Homo sapiens (human) ]

    Gene ID: 54585, updated on 5-May-2024

    Summary

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    Official Symbol
    LZTFL1provided by HGNC
    Official Full Name
    leucine zipper transcription factor like 1provided by HGNC
    Primary source
    HGNC:HGNC:6741
    See related
    Ensembl:ENSG00000163818 MIM:606568; AllianceGenome:HGNC:6741
    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
    BBS17
    Summary
    This gene encodes a ubiquitously expressed protein that localizes to the cytoplasm. This protein interacts with Bardet-Biedl Syndrome (BBS) proteins and, through its interaction with BBS protein complexes, regulates protein trafficking to the ciliary membrane. Nonsense mutations in this gene cause a form of Bardet-Biedl Syndrome; a ciliopathy characterized in part by polydactyly, obesity, cognitive impairment, hypogonadism, and kidney failure. This gene may also function as a tumor suppressor; possibly by interacting with E-cadherin and the actin cytoskeleton and thereby regulating the transition of epithelial cells to mesenchymal cells. [provided by RefSeq, Aug 2020]
    Annotation information
    Note: This gene has been reviewed for its involvement in coronavirus biology, and is locus in the vicinity of disease-associated variant(s).
    Expression
    Broad expression in testis (RPKM 18.3), thyroid (RPKM 11.9) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LZTFL1 in Genome Data Viewer
    Location:
    3p21.31
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (45823316..45915724, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (45838956..45931607, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (45864808..45957216, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene SAC1 like phosphatidylinositide phosphatase Neighboring gene RNA, 7SL, cytoplasmic 145, pseudogene Neighboring gene solute carrier family 6 member 20 Neighboring gene uncharacterized LOC107986082 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:45859284-45860483 Neighboring gene uncharacterized LOC124909374 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:45921781-45921937 Neighboring gene CCR9 promoter region Neighboring gene succinate dehydrogenase complex subunit D pseudogene 4 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:45956761-45957960 Neighboring gene C-C motif chemokine receptor 9 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:45979037-45980236 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:45989039-45989208 Neighboring gene FYVE and coiled-coil domain autophagy adaptor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19787 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46009167-46009806 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46009807-46010446 Neighboring gene C-X-C motif chemokine receptor 6 Neighboring gene Sharpr-MPRA regulatory region 2695 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:46029541-46030041 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46034569-46035069 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:46037115-46037614 Neighboring gene uncharacterized LOC105377063

    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. Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus. Downes DJ, et al. Nat Genet, 2021 Nov. PMID 34737427, Free PMC Article
    2. Leucine zipper transcription factor-like 1 binds adaptor protein complex-1 and 2 and participates in trafficking of transferrin receptor 1. Promchan K, et al. PLoS One, 2020. PMID 31895934, Free PMC Article
    3. Tumor suppressive functions of LZTFL1 in hepatocellular carcinoma. Li S, et al. Onco Targets Ther, 2019. PMID 31371991, Free PMC Article
    4. LZTFL1 Upregulated by All-Trans Retinoic Acid during CD4+ T Cell Activation Enhances IL-5 Production. Jiang H, et al. J Immunol, 2016 Feb 1. PMID 26700766, Free PMC Article
    5. LZTFL1 suppresses lung tumorigenesis by maintaining differentiation of lung epithelial cells. Wei Q, et al. Oncogene, 2016 May 19. PMID 26364604, Free PMC Article

    See all (46) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Association of 3p21.31 Locus (CXCR6 and LZTFL1) with COVID-19 Outcomes in Brazilian Hospitalyzed Subjects.
      Title: Association of 3p21.31 Locus (CXCR6 and LZTFL1) with COVID-19 Outcomes in Brazilian Hospitalyzed Subjects.
    2. LZTFL1 inhibits kidney tumor cell growth by destabilizing AKT through ZNRF1-mediated ubiquitin proteosome pathway.
      Title: LZTFL1 inhibits kidney tumor cell growth by destabilizing AKT through ZNRF1-mediated ubiquitin proteosome pathway.
    3. Host genetic loci LZTFL1 and CCL2 associated with SARS-CoV-2 infection and severity of COVID-19.
      Title: Host genetic loci LZTFL1 and CCL2 associated with SARS-CoV-2 infection and severity of COVID-19.
    4. CRISPRi links COVID-19 GWAS loci to LZTFL1 and RAVER1.
      Title: CRISPRi links COVID-19 GWAS loci to LZTFL1 and RAVER1.
    5. lncRNA SNHG6 promotes hepatocellular carcinoma progression by interacting with HNRNPL/PTBP1 to facilitate SETD7/LZTFL1 mRNA destabilization.
      Title: lncRNA SNHG6 promotes hepatocellular carcinoma progression by interacting with HNRNPL/PTBP1 to facilitate SETD7/LZTFL1 mRNA destabilization.
    6. Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus.
      Title: Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus.
    7. Limited time window for retinal gene therapy in a preclinical model of ciliopathy.
      Title: Limited time window for retinal gene therapy in a preclinical model of ciliopathy.
    8. LZTFL1 was identified as a novel target gene of miR-21. Knockdown of LZTFL1 overcame the suppression of miR-21 inhibitor on cell proliferation, metastasis and the expression of epithelial-mesenchymal transition markers in breast cancer cells.
      Title: microRNA-21 promotes breast cancer proliferation and metastasis by targeting LZTFL1.
    9. LZTFL1 inhibits lung tumorigenesis
      Title: LZTFL1 suppresses lung tumorigenesis by maintaining differentiation of lung epithelial cells.
    10. these data indicate that LZTFL1 modulates T cell activation and IL-5 levels.
      Title: LZTFL1 Upregulated by All-Trans Retinoic Acid during CD4+ T Cell Activation Enhances IL-5 Production.
    Submit: New GeneRIF Correction See all GeneRIFs (16)

    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
    Bardet-Biedl syndrome 17
    MedGen: C3714980 OMIM: 615994 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
    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

    • FLJ36386

    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 protein-containing complex binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in flagellated sperm motility IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of protein localization to ciliary membrane IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of protein localization to cilium IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of protein localization to cilium IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in spermatogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cilium IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in manchette IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    leucine zipper transcription factor-like protein 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.

    Genomic

    1. NG_033917.1 RefSeqGene

      Range
      78606..97409
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001276378.2 → NP_001263307.1  leucine zipper transcription factor-like protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001263307.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains a distinct 5' UTR and has multiple coding region differences, compared to variant 1. These differences cause translation initiation at a downstream in-frame AUG and result in an isoform (2) with a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC098476, AK093705, BX112707
      Consensus CDS
      CCDS63608.1
      UniProtKB/TrEMBL
      H7C488
      Related
      ENSP00000506925.1, ENST00000684620.1

    2. NM_001276379.2 → NP_001263308.1  leucine zipper transcription factor-like protein 1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains a distinct 5' UTR, has multiple coding region differences, and initiates translation at an alternate start codon compared to variant 1. The encoded isoform (3) is shorter and has distinct N- and C-termini, compared to isoform 1.
      Source sequence(s)
      AC098476, AK303416, BX112707, CN429018, DC410047
      Consensus CDS
      CCDS63609.1
      UniProtKB/TrEMBL
      A0A8V8TP88
      Related
      ENSP00000441784.1, ENST00000539217.5
      Conserved Domains (1) summary
      pfam15294
      Location:40 → 255
      Leu_zip; Leucine zipper

    3. NM_001386451.1 → NP_001373380.1  leucine zipper transcription factor-like protein 1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC098476, AC099782
      Consensus CDS
      CCDS63608.1
      UniProtKB/TrEMBL
      H7C488
      Conserved Domains (1) summary
      pfam15294
      Location:3 → 277
      Leu_zip; Leucine zipper

    4. NM_001386452.1 → NP_001373381.1  leucine zipper transcription factor-like protein 1 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC098476, AC099782
      UniProtKB/TrEMBL
      A0A8V8TP88
      Related
      ENSP00000514188.1, ENST00000699187.1
      Conserved Domains (1) summary
      pfam15294
      Location:20 → 259
      Leu_zip; Leucine zipper

    5. NM_001405920.1 → NP_001392849.1  leucine zipper transcription factor-like protein 1 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC098476, AC099782

    6. NM_001405921.1 → NP_001392850.1  leucine zipper transcription factor-like protein 1 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC098476, AC099782

    7. NM_001405922.1 → NP_001392851.1  leucine zipper transcription factor-like protein 1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC098476, AC099782
      Consensus CDS
      CCDS63608.1

    8. NM_001405923.1 → NP_001392852.1  leucine zipper transcription factor-like protein 1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC098476, AC099782

    9. NM_001405924.1 → NP_001392853.1  leucine zipper transcription factor-like protein 1 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC098476, AC099782
      Related
      ENSP00000416083.2, ENST00000440576.2

    10. NM_001405925.1 → NP_001392854.1  leucine zipper transcription factor-like protein 1 isoform 8

      Status: REVIEWED

      Source sequence(s)
      AC098476, AC099782

    11. NM_001405926.1 → NP_001392855.1  leucine zipper transcription factor-like protein 1 isoform 9

      Status: REVIEWED

      Source sequence(s)
      AC098476, AC099782

    12. NM_001405927.1 → NP_001392856.1  leucine zipper transcription factor-like protein 1 isoform 9

      Status: REVIEWED

      Source sequence(s)
      AC098476, AC099782

    13. NM_001405928.1 → NP_001392857.1  leucine zipper transcription factor-like protein 1 isoform 9

      Status: REVIEWED

      Source sequence(s)
      AC098476, AC099782

    14. NM_020347.4 → NP_065080.1  leucine zipper transcription factor-like protein 1 isoform 1

      See identical proteins and their annotated locations for NP_065080.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC098476, AJ297351, BX112707, HY159348
      Consensus CDS
      CCDS2731.1
      UniProtKB/Swiss-Prot
      B3KSI9, B4E0K7, Q8TC61, Q9NQ48, Q9NQ56
      UniProtKB/TrEMBL
      A0A8V8TP88
      Related
      ENSP00000296135.6, ENST00000296135.11
      Conserved Domains (1) summary
      pfam15294
      Location:20 → 294
      Leu_zip; Leucine zipper

    RNA

    1. NR_075080.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC098476, AJ297351, BX112707, DA408809
      Related
      ENST00000699186.1

    2. NR_170121.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC099782
      Related
      ENST00000699188.1

    3. NR_175976.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC098476, AC099782

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      45823316..45915724 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047448366.1 → XP_047304322.1  leucine zipper transcription factor-like protein 1 isoform X2

    2. XM_047448365.1 → XP_047304321.1  leucine zipper transcription factor-like protein 1 isoform X1

    3. XM_017006645.3 → XP_016862134.1  leucine zipper transcription factor-like protein 1 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      45838956..45931607 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054346946.1 → XP_054202921.1  leucine zipper transcription factor-like protein 1 isoform X2

    2. XM_054346945.1 → XP_054202920.1  leucine zipper transcription factor-like protein 1 isoform X1

    3. XM_054346947.1 → XP_054202922.1  leucine zipper transcription factor-like protein 1 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NQ48.1 GenPept UniProtKB/Swiss-Prot:Q9NQ48

    Gene LinkOut

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

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