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

Gene ID: 148534, updated on 5-Mar-2024

Summary

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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
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Genomic context

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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

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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. 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) consortium. Wu JH, et al. Circ Cardiovasc Genet, 2013 Apr. PMID 23362303, Free PMC Article
  2. Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV. Stukalov A, et al. Nature, 2021 Jun. PMID 33845483
  3. Ubiquitin-mediated proteolysis of HuR by heat shock. Abdelmohsen K, et al. EMBO J, 2009 May 6. PMID 19322201, Free PMC Article
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. Rose JE, et al. Mol Med, 2010 Jul-Aug. PMID 20379614, Free PMC Article
  5. Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei. Fasci D, et al. Mol Cell Proteomics, 2018 Oct. PMID 30021884, Free PMC Article

See all (13) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
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
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

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

Readthrough TLCD4-RWDD3

Readthrough gene: TLCD4-RWDD3, Included gene: RWDD3

Homology

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

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

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_001199679.2 → NP_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:44 → 246
    TLC; TRAM, LAG1 and CLN8 homology domains

  2. NM_152487.3 → NP_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:44 → 246
    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)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96MV1.1 GenPept UniProtKB/Swiss-Prot:Q96MV1

Gene LinkOut

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

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