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

Gene ID: 83723, updated on 5-Mar-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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Location:
16p11.2
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (30024427..30053040, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (30307060..30335676, complement)
105.20220307 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
  • 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_2023_10

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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