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

Gene ID: 54585, updated on 3-Apr-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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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
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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

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