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    TLCD1 TLC domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 116238, updated on 28-Oct-2024

    Summary

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    Official Symbol
    TLCD1provided by HGNC
    Official Full Name
    TLC domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:25177
    See related
    Ensembl:ENSG00000160606 MIM:620966; AllianceGenome:HGNC:25177
    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
    Summary
    Involved in several processes, including membrane assembly; phospholipid homeostasis; and regulation of membrane lipid distribution. Located in plasma membrane. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in ovary (RPKM 8.5), lymph node (RPKM 6.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TLCD1 in Genome Data Viewer
    Location:
    17q11.2
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (28724348..28727937, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (29667155..29669739, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (27051366..27053950, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein L23a Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8350 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:27052063-27052786 Neighboring gene small nucleolar RNA, C/D box 42A Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:27052787-27053510 Neighboring gene small nucleolar RNA, C/D box 4B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:27053511-27054234 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:27054959-27055682 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:27055683-27056406 Neighboring gene NIMA related kinase 8 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11943 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:27064492-27065026 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11946 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11947 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11948 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11950 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8352 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11951 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:27070105-27071105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8354 Neighboring gene TNF receptor associated factor 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:27074109-27075108

    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 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. TLCD1 and TLCD2 regulate cellular phosphatidylethanolamine composition and promote the progression of non-alcoholic steatohepatitis. Petkevicius K, et al. Nat Commun, 2022 Oct 14. PMID 36241646, Free PMC Article
    2. Calfacilitin is a calcium channel modulator essential for initiation of neural plate development. Papanayotou C, et al. Nat Commun, 2013. PMID 23673622, Free PMC Article
    3. Membrane fluidity is regulated by the C. elegans transmembrane protein FLD-1 and its human homologs TLCD1/2. Ruiz M, et al. Elife, 2018 Dec 4. PMID 30509349, Free PMC Article
    4. TRAM, LAG1 and CLN8: members of a novel family of lipid-sensing domains? Winter E, et al. Trends Biochem Sci, 2002 Aug. PMID 12151215
    5. Comparative proximity biotinylation implicates the small GTPase RAB18 in sterol mobilization and biosynthesis. Kiss RS, et al. J Biol Chem, 2023 Nov. PMID 37774976, Free PMC Article

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TLCD1 and TLCD2 regulate cellular phosphatidylethanolamine composition and promote the progression of non-alcoholic steatohepatitis.
      Title: TLCD1 and TLCD2 regulate cellular phosphatidylethanolamine composition and promote the progression of non-alcoholic steatohepatitis.
    2. inhibition of FLD-1 or TLCD1/2 prevents lipotoxicity by allowing increased levels of membrane phospholipids that contain fluidizing long-chain polyunsaturated fatty acids.
      Title: Membrane fluidity is regulated by the C. elegans transmembrane protein FLD-1 and its human homologs TLCD1/2.
    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

    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

    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 membrane assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in membrane assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in phospholipid homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in phospholipid homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in plasma membrane organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in plasma membrane organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of membrane lipid distribution IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of membrane lipid distribution IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in plasma membrane 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 1
    Names
    calfacilitin

    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_001160407.2 → NP_001153879.1  TLC domain-containing protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001153879.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC010761, BC014072, BF478215, BX106421
      Consensus CDS
      CCDS54102.1
      UniProtKB/Swiss-Prot
      Q96CP7
      Related
      ENSP00000378391.3, ENST00000394933.7
      Conserved Domains (1) summary
      smart00724
      Location:20 → 187
      TLC; TRAM, LAG1 and CLN8 homology domains

    2. NM_138463.4 → NP_612472.1  TLC domain-containing protein 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_612472.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC010761, BC014072, BF478215, CA453962
      Consensus CDS
      CCDS11242.1
      UniProtKB/Swiss-Prot
      A8MYP9, Q96CP7
      Related
      ENSP00000292090.3, ENST00000292090.8
      Conserved Domains (1) summary
      smart00724
      Location:41 → 234
      TLC; TRAM, LAG1 and CLN8 homology domains

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    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
      28724348..28727937 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006721671.5 → XP_006721734.1  TLC domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      K7ELX5
      Related
      ENSP00000466264.1, ENST00000580518.1
      Conserved Domains (1) summary
      smart00724
      Location:7 → 163
      TLC; TRAM, LAG1 and CLN8 homology domains

    2. XM_047435299.1 → XP_047291255.1  TLC domain-containing protein 1 isoform X2

    3. XM_011524278.4 → XP_011522580.1  TLC domain-containing protein 1 isoform X1

      Conserved Domains (1) summary
      smart00724
      Location:41 → 183
      TLC; TRAM, LAG1 and CLN8 homology domains

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      29667155..29669739 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314959.1 → XP_054170934.1  TLC domain-containing protein 1 isoform X2

    2. XM_054314958.1 → XP_054170933.1  TLC domain-containing protein 1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96CP7.1 GenPept UniProtKB/Swiss-Prot:Q96CP7

    Gene LinkOut

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

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