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    TLCD3B TLC domain containing 3B [ Homo sapiens (human) ]

    Gene ID: 83723, updated on 2-Nov-2024

    Summary

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    Official Symbol
    TLCD3Bprovided by HGNC
    Official Full Name
    TLC domain containing 3Bprovided by HGNC
    Primary source
    HGNC:HGNC:25295
    See related
    Ensembl:ENSG00000149926 MIM:615175; AllianceGenome:HGNC:25295
    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
    CORD22; FAM57B; FP1188
    Summary
    This gene encodes a transmembrane protein, which may be a likely target of peroxisome proliferator-activated receptor gamma (PPAR-gamma). The product of the orthologous gene in mouse is related to obesity. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
    Expression
    Restricted expression toward testis (RPKM 12.4) See more
    Orthologs
    mouse all
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    Genomic context

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    See TLCD3B in Genome Data Viewer
    Location:
    16p11.2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (30024427..30053040, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (30307060..30335676, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (30035748..30047851, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30004428-30004928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30004929-30005429 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10686 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10687 Neighboring gene HIRA interacting protein 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30015046-30015830 Neighboring gene INO80 complex subunit E Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7347 Neighboring gene double C2 domain alpha Neighboring gene chromosome 16 open reading frame 92 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30039801-30040645 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7348 Neighboring gene MPRA-validated peak2562 silencer Neighboring gene uncharaterized LOC112694756 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30064875-30065853 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:30065854-30066831 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:30076132-30076912 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7349 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7350 Neighboring gene aldolase, fructose-bisphosphate A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10688 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7351 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10689 Neighboring gene protein phosphatase 4 catalytic subunit

    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. Ceramide synthase TLCD3B is a novel gene associated with human recessive retinal dystrophy. Bertrand RE, et al. Genet Med, 2021 Mar. PMID 33077892, Free PMC Article
    2. Fam57b (family with sequence similarity 57, member B), a novel peroxisome proliferator-activated receptor γ target gene that regulates adipogenesis through ceramide synthesis. Yamashita-Sugahara Y, et al. J Biol Chem, 2013 Feb 15. PMID 23275342, Free PMC Article
    3. Large-scale cDNA transfection screening for genes related to cancer development and progression. Wan D, et al. Proc Natl Acad Sci U S A, 2004 Nov 2. PMID 15498874, Free PMC Article
    4. Full-length transcriptome analysis of human retina-derived cell lines ARPE-19 and Y79 using the vector-capping method. Oshikawa M, et al. Invest Ophthalmol Vis Sci, 2011 Aug 22. PMID 21697133
    5. ZFP36L2 is a cell cycle-regulated CCCH protein necessary for DNA lesion-induced S-phase arrest. Noguchi A, et al. Biol Open, 2018 Mar 12. PMID 29449217, Free PMC Article

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Ceramide synthase TLCD3B is a novel gene associated with human recessive retinal dystrophy.
      Title: Ceramide synthase TLCD3B is a novel gene associated with human recessive retinal dystrophy.
    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

    Associated conditions

    Description Tests
    Cone-rod dystrophy 22
    MedGen: C5561989 OMIM: 619531 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    Biological insights from 108 schizophrenia-associated genetic loci.
    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ40208, DKFZp434I2117

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables sphingosine N-acyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in ceramide biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in lipid homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of fat cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		  
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    ceramide synthase
    Names
    TLC domain 3B
    TLC domain ceramide synthase 3B
    TLC domain-containing protein 3B
    epididymis secretory sperm binding protein
    family with sequence similarity 57 member B
    protein FAM57B

    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_001318504.2 → NP_001305433.1  ceramide synthase isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. It encodes isoform 2, which has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AL136777, BM676198
      Consensus CDS
      CCDS81967.1
      UniProtKB/Swiss-Prot
      Q71RH2
      Related
      ENSP00000279389.4, ENST00000279389.8
      Conserved Domains (1) summary
      smart00724
      Location:15 → 211
      TLC; TRAM, LAG1 and CLN8 homology domains

    2. NM_001352173.2 → NP_001339102.1  ceramide synthase isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC093512
      Conserved Domains (1) summary
      smart00724
      Location:126 → 347
      TLC; TRAM, LAG1 and CLN8 homology domains

    3. NM_031478.6 → NP_113666.2  ceramide synthase isoform 1

      See identical proteins and their annotated locations for NP_113666.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform.
      Source sequence(s)
      AB593089, AC093512, AL535138, BM676198, BQ185065
      Consensus CDS
      CCDS10667.2
      UniProtKB/Swiss-Prot
      Q71RH2, Q9H0J1
      UniProtKB/TrEMBL
      F1T0F5
      Related
      ENSP00000369863.4, ENST00000380495.9
      Conserved Domains (1) summary
      smart00724
      Location:40 → 261
      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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      30024427..30053040 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047434736.1 → XP_047290692.1  ceramide synthase isoform X2

    2. XM_005255614.4 → XP_005255671.1  ceramide synthase isoform X2

      See identical proteins and their annotated locations for XP_005255671.1

      Conserved Domains (1) summary
      smart00724
      Location:40 → 261
      TLC; TRAM, LAG1 and CLN8 homology domains

    3. XM_017023752.2 → XP_016879241.1  ceramide synthase isoform X2

      Conserved Domains (1) summary
      smart00724
      Location:40 → 261
      TLC; TRAM, LAG1 and CLN8 homology domains

    4. XM_005255613.4 → XP_005255670.1  ceramide synthase isoform X2

      See identical proteins and their annotated locations for XP_005255670.1

      Conserved Domains (1) summary
      smart00724
      Location:40 → 261
      TLC; TRAM, LAG1 and CLN8 homology domains

    5. XM_017023751.2 → XP_016879240.1  ceramide synthase isoform X2

      Conserved Domains (1) summary
      smart00724
      Location:40 → 261
      TLC; TRAM, LAG1 and CLN8 homology domains

    6. XM_017023750.3 → XP_016879239.1  ceramide synthase isoform X2

      Conserved Domains (1) summary
      smart00724
      Location:40 → 261
      TLC; TRAM, LAG1 and CLN8 homology domains

    7. XM_024450464.2 → XP_024306232.1  ceramide synthase isoform X1

      Conserved Domains (1) summary
      smart00724
      Location:75 → 296
      TLC; TRAM, LAG1 and CLN8 homology domains

    8. XM_024450466.2 → XP_024306234.1  ceramide synthase isoform X3

      Conserved Domains (1) summary
      smart00724
      Location:15 → 211
      TLC; TRAM, LAG1 and CLN8 homology domains

    9. XM_017023754.2 → XP_016879243.1  ceramide synthase isoform X3

      UniProtKB/Swiss-Prot
      Q71RH2
      Conserved Domains (1) summary
      smart00724
      Location:15 → 211
      TLC; TRAM, LAG1 and CLN8 homology domains

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      30307060..30335676 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314100.1 → XP_054170075.1  ceramide synthase isoform X2

    2. XM_054314099.1 → XP_054170074.1  ceramide synthase isoform X2

    3. XM_054314096.1 → XP_054170071.1  ceramide synthase isoform X2

    4. XM_054314097.1 → XP_054170072.1  ceramide synthase isoform X2

    5. XM_054314098.1 → XP_054170073.1  ceramide synthase isoform X2

    6. XM_054314095.1 → XP_054170070.1  ceramide synthase isoform X1

    7. XM_054314101.1 → XP_054170076.1  ceramide synthase isoform X2

    8. XM_054314103.1 → XP_054170078.1  ceramide synthase isoform X3

    9. XM_054314102.1 → XP_054170077.1  ceramide synthase isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q71RH2.1 GenPept UniProtKB/Swiss-Prot:Q71RH2

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