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

Gene ID: 116238, updated on 5-Mar-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 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, Apr 2022]
Expression
Ubiquitous expression in ovary (RPKM 8.5), lymph node (RPKM 6.1) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
17q11.2
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (28724348..28727937, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (29667155..29669739, complement)
105.20220307 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
  • 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. Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV. Stukalov A, et al. Nature, 2021 Jun. PMID 33845483

See all (12) 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_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
    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

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