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    TLCD3A TLC domain containing 3A [ Homo sapiens (human) ]

    Gene ID: 79850, updated on 3-Apr-2024

    Summary

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    Official Symbol
    TLCD3Aprovided by HGNC
    Official Full Name
    TLC domain containing 3Aprovided by HGNC
    Primary source
    HGNC:HGNC:29646
    See related
    Ensembl:ENSG00000167695 MIM:611627; AllianceGenome:HGNC:29646
    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
    CT120; FAM57A
    Summary
    The protein encoded by this gene is a membrane-associated protein that promotes lung carcinogenesis. The encoded protein may be involved in amino acid transport and glutathione metabolism since it can interact with a solute carrier family member (SLC3A2) and an isoform of gamma-glutamyltranspeptidase-like 3. An alternatively spliced variant encoding a protein that lacks a 32 aa internal segment showed the opposite effect, inhibiting lung cancer cell growth. Knockdown of this gene also inhibited lung carcinogenesis and tumor cell growth. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2015]
    Expression
    Broad expression in skin (RPKM 26.1), esophagus (RPKM 9.7) and 18 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TLCD3A in Genome Data Viewer
    Location:
    17p13.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (732596..742968)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (617519..628045)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (635836..646208)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene VPS53 subunit of GARP complex Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:560426-561625 Neighboring gene ribosomal protein S4X pseudogene 17 Neighboring gene Sharpr-MPRA regulatory region 8461 Neighboring gene Sharpr-MPRA regulatory region 15051 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:610400-610605 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11438 Neighboring gene uncharacterized LOC124903893 Neighboring gene Sharpr-MPRA regulatory region 11717 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7941 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7942 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7943 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11439 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7944 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7945 Neighboring gene gem nuclear organelle associated protein 4 Neighboring gene diazepam binding inhibitor-like 5, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11440 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:685572-686120 Neighboring gene glyoxalase domain containing 4 Neighboring gene mitochondrial rRNA methyltransferase 3

    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. FAM57A (Family with Sequence Similarity 57 Member A) Is a Cell-Density-Regulated Protein and Promotes the Proliferation and Migration of Cervical Cancer Cells. Yang D, et al. Cells, 2022 Oct 21. PMID 36291175, Free PMC Article
    2. Silencing of CT120 by antisense oligonucleotides could inhibit the lung cancer cells growth. Li Z, et al. Ir J Med Sci, 2010 Jun. PMID 20024628
    3. Inhibitory effect of CT120B, an alternative splice variant of CT120A, on lung cancer cell growth. Pan DN, et al. Acta Biochim Biophys Sin (Shanghai), 2005 Sep. PMID 16143812
    4. Down-regulation of CT120A by RNA interference suppresses lung cancer cells growth and sensitizes to ultraviolet-induced apoptosis. Pan D, et al. Cancer Lett, 2006 Apr 8. PMID 15927361
    5. Altered gene expression profiles of NIH3T3 cells regulated by human lung cancer associated gene CT120. He XH, et al. Cell Res, 2004 Dec. PMID 15625016

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. FAM57A (Family with Sequence Similarity 57 Member A) Is a Cell-Density-Regulated Protein and Promotes the Proliferation and Migration of Cervical Cancer Cells.
      Title: FAM57A (Family with Sequence Similarity 57 Member A) Is a Cell-Density-Regulated Protein and Promotes the Proliferation and Migration of Cervical Cancer Cells.
    2. The researchers found evidence that CT120 may be a key factor in tumor progression and that down-regulation of CT120 may be an effective treatment for lung neoplasms.
      Title: Silencing of CT120 by antisense oligonucleotides could inhibit the lung cancer cells growth.
    3. Molecular cloning and characterization of this novel membrane-associated gene involved in amino acid transport and glutathione metabolism
      Title: Molecular cloning and characterization of CT120, a novel membrane-associated gene involved in amino acid transport and glutathione metabolism.
    4. CT120B overexpression resulted in reduction of cell growth rate & inhibited tumorigenecity & anchorage-independent growth; findings suggest that the delayed G1/S phase transition might contribute to the inhibitory activities of CT120B on cell growth
      Title: Inhibitory effect of CT120B, an alternative splice variant of CT120A, on lung cancer cell growth.
    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
    Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ22282

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in lipid homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    TLC domain-containing protein 3A
    Names
    family with sequence similarity 57 member A
    membrane protein expressed in epithelial-like lung adenocarcinoma
    protein FAM57A

    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_001318006.2 → NP_001304935.1  TLC domain-containing protein 3A isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2, also known as CT120B) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AA055841, AC087392, BC026023
      Consensus CDS
      CCDS82031.1
      UniProtKB/Swiss-Prot
      Q8TBR7
      Related
      ENSP00000301324.8, ENST00000301324.8
      Conserved Domains (1) summary
      smart00724
      Location:33 → 217
      TLC; TRAM, LAG1 and CLN8 homology domains

    2. NM_001318007.2 → NP_001304936.1  TLC domain-containing protein 3A isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate exon compared to variant 1, that causes a frameshift. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AA055841, AC087392, AK025935, BX389422, CN259418
      UniProtKB/Swiss-Prot
      Q8TBR7

    3. NM_001318008.2 → NP_001304937.1  TLC domain-containing protein 3A isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks two alternate exons compared to variant 1, that causes a frameshift. The resulting isoform (4) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AA055841, AC087392, AK025935, CN259418
      Consensus CDS
      CCDS82032.1
      UniProtKB/TrEMBL
      I3L336
      Related
      ENSP00000460150.1, ENST00000572018.5

    4. NM_024792.3 → NP_079068.1  TLC domain-containing protein 3A isoform 1

      See identical proteins and their annotated locations for NP_079068.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1, also known as CT120A) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AA055841, AC087392, AK025935, CN259418
      Consensus CDS
      CCDS10996.1
      UniProtKB/Swiss-Prot
      A8K7Q0, Q7Z464, Q8TBR7, Q96D97, Q9H6H3
      Related
      ENSP00000312017.7, ENST00000308278.13
      Conserved Domains (1) summary
      smart00724
      Location:33 → 249
      TLC; TRAM, LAG1 and CLN8 homology domains

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      732596..742968
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      617519..628045
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054317265.1 → XP_054173240.1  TLC domain-containing protein 3A isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8TBR7.2 GenPept UniProtKB/Swiss-Prot:Q8TBR7

    Gene LinkOut

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

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