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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
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Genomic context

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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

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