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    TLCD4 TLC domain containing 4 [ Homo sapiens (human) ]

    Gene ID: 148534, updated on 3-Dec-2023

    Summary

    Official Symbol
    TLCD4provided by HGNC
    Official Full Name
    TLC domain containing 4provided by HGNC
    Primary source
    HGNC:HGNC:26477
    See related
    Ensembl:ENSG00000152078 AllianceGenome:HGNC:26477
    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
    Also known as
    TMEM56
    Summary
    Predicted to be involved in lipid homeostasis. Predicted to be integral component of membrane. Predicted to be active in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in liver (RPKM 27.2), heart (RPKM 9.3) and 19 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See TLCD4 in Genome Data Viewer
    Location:
    1p21.3
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (95092517..95197607)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (94940904..95045995)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (95558073..95663163)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ALG14 UDP-N-acetylglucosaminyltransferase subunit Neighboring gene uncharacterized LOC105378863 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:95508724-95509332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95509333-95509941 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1352 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1353 Neighboring gene ALG14 antisense RNA 1 Neighboring gene CRISPRi-validated cis-regulatory element chr1.7351 Neighboring gene CRISPRi-validated cis-regulatory element chr1.7352 Neighboring gene CRISPRi-validated cis-regulatory element chr1.7353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1354 Neighboring gene CRISPRi-validated cis-regulatory element chr1.7357 Neighboring gene CRISPRi-validated cis-regulatory element chr1.7358 Neighboring gene CRISPRi-validated cis-regulatory element chr1.7359 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:95582918-95583064 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1104 Neighboring gene TLCD4-RWDD3 readthrough Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95600812-95601312 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95601313-95601813 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:95602368-95602560 Neighboring gene RWDD3 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95682171-95682671 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1106 Neighboring gene RWD domain containing 3 Neighboring gene MPRA-validated peak328 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:95762972-95763562 Neighboring gene Sharpr-MPRA regulatory region 5488 Neighboring gene uncharacterized LOC105378864 Neighboring gene long intergenic non-protein coding RNA 1760

    Genomic regions, transcripts, and products

    Expression

    • 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

    Phenotypes

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies novel loci associated with concentrations of four plasma phospholipid fatty acids in the de novo lipogenesis pathway: results from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortiu
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Readthrough TLCD4-RWDD3

    Readthrough gene: TLCD4-RWDD3, Included gene: RWDD3

    Clone Names

    • FLJ31842, MGC102912

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
     
    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 cellular_component ND
    No biological Data available
    more info
     
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    TLC domain-containing protein 4
    Names
    transmembrane protein 56

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001199679.2NP_001186608.1  TLC domain-containing protein 4

      See identical proteins and their annotated locations for NP_001186608.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC092802, AC095033, AK126344, BC108263, BC139737, BQ575814
      Consensus CDS
      CCDS753.1
      UniProtKB/Swiss-Prot
      B2RPI2, D3DT48, Q96MV1
      Conserved Domains (1) summary
      smart00724
      Location:44246
      TLC; TRAM, LAG1 and CLN8 homology domains
    2. NM_152487.3NP_689700.1  TLC domain-containing protein 4

      See identical proteins and their annotated locations for NP_689700.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC092802, AC095033
      Consensus CDS
      CCDS753.1
      UniProtKB/Swiss-Prot
      B2RPI2, D3DT48, Q96MV1
      Related
      ENSP00000359222.4, ENST00000370203.9
      Conserved Domains (1) summary
      smart00724
      Location:44246
      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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      95092517..95197607
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      94940904..95045995
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)