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    TMEM38B transmembrane protein 38B [ Homo sapiens (human) ]

    Gene ID: 55151, updated on 5-Mar-2024

    Summary

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    Official Symbol
    TMEM38Bprovided by HGNC
    Official Full Name
    transmembrane protein 38Bprovided by HGNC
    Primary source
    HGNC:HGNC:25535
    See related
    Ensembl:ENSG00000095209 MIM:611236; AllianceGenome:HGNC:25535
    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
    OI14; TRICB; TRIC-B; C9orf87; D4Ertd89e; bA219P18.1
    Summary
    This gene encodes an intracellular monovalent cation channel that functions in maintenance of intracellular calcium release. Mutations in this gene may be associated with autosomal recessive osteogenesis. [provided by RefSeq, Oct 2012]
    Expression
    Broad expression in thyroid (RPKM 13.5), testis (RPKM 9.6) and 23 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    9q31.2
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (105694541..105776629)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (117869221..117951308)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (108456822..108538910)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28744 Neighboring gene NANOG hESC enhancer GRCh37_chr9:108355386-108355925 Neighboring gene FKTN antisense RNA 1 Neighboring gene GATA motif-containing MPRA enhancer 228 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:108413980-108414542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28745 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28746 Neighboring gene fukutin Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20154 Neighboring gene uncharacterized LOC107987107 Neighboring gene serine and arginine rich splicing factor 10 pseudogene Neighboring gene Sharpr-MPRA regulatory region 1451 Neighboring gene MPRA-validated peak7316 silencer Neighboring gene TAL bHLH transcription factor 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:108544378-108545028 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:108545029-108545679 Neighboring gene DEP domain containing 1 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:108597740-108598240 Neighboring gene solute carrier family 25 member 6 pseudogene 5 Neighboring gene uncharacterized LOC107987108 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:108720067-108720622 Neighboring gene uncharacterized LOC107987109

    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. Absence of the ER Cation Channel TMEM38B/TRIC-B Disrupts Intracellular Calcium Homeostasis and Dysregulates Collagen Synthesis in Recessive Osteogenesis Imperfecta. Cabral WA, et al. PLoS Genet, 2016 Jul. PMID 27441836, Free PMC Article
    2. Two novel mutations in TMEM38B result in rare autosomal recessive osteogenesis imperfecta. Lv F, et al. J Hum Genet, 2016 Jun. PMID 26911354
    3. A deletion mutation in TMEM38B associated with autosomal recessive osteogenesis imperfecta. Volodarsky M, et al. Hum Mutat, 2013 Apr. PMID 23316006
    4. Study of autosomal recessive osteogenesis imperfecta in Arabia reveals a novel locus defined by TMEM38B mutation. Shaheen R, et al. J Med Genet, 2012 Oct. PMID 23054245
    5. Meta-analysis of genome-wide association data identifies two loci influencing age at menarche. Perry JR, et al. Nat Genet, 2009 Jun. PMID 19448620, Free PMC Article

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Absence of TRIC-B from type XIV Osteogenesis Imperfecta osteoblasts alters cell adhesion and mitochondrial function - A multi-omics study.
      Title: Absence of TRIC-B from type XIV Osteogenesis Imperfecta osteoblasts alters cell adhesion and mitochondrial function - A multi-omics study.
    2. TMEM38B mutations could lead to a rare form of OI, with an autosomal recessive pattern of inheritance. We identified two novel mutations (c.455-7T>G in intron 3 and c.507G>A in exon 4) in TMEM38B in three Chinese children with OI. The two mutations created a new acceptor splice site (p.R151_G152insVL) and a novel downstream termination codon (p.W169X), respectively
      Title: Two novel mutations in TMEM38B result in rare autosomal recessive osteogenesis imperfecta.
    3. Absence of TMEM38B causes osteogenesis imperfecta by dysregulation of calcium flux kinetics in the endoplasmic reticulum, impacting multiple collagen-specific chaperones and modifying enzymes.
      Title: Absence of the ER Cation Channel TMEM38B/TRIC-B Disrupts Intracellular Calcium Homeostasis and Dysregulates Collagen Synthesis in Recessive Osteogenesis Imperfecta.
    4. A deletion mutation in TMEM38B associated with autosomal recessive osteogenesis imperfecta.
      Title: A deletion mutation in TMEM38B associated with autosomal recessive osteogenesis imperfecta.
    5. TMEM38B is a novel candidate gene for autosomal recessive Osteogenesis imperfecta (OI). Future studies are needed to explore fully the contribution of this gene to autosomal recessive Osteogenesis imperfecta (OI) in other populations.
      Title: Study of autosomal recessive osteogenesis imperfecta in Arabia reveals a novel locus defined by TMEM38B mutation.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study.
    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
    Osteogenesis imperfecta type 14
    MedGen: C3554428 OMIM: 615066 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies protein quantitative trait loci (pQTLs).
    EBI GWAS Catalog
    Genome-wide association and longitudinal analyses reveal genetic loci linking pubertal height growth, pubertal timing and childhood adiposity.
    EBI GWAS Catalog
    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association data identifies two loci influencing age at menarche.
    EBI GWAS Catalog
    Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
    EBI GWAS Catalog
    Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.
    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 is identified to have a physical interaction with transmembrane protein 38B (TMEM38B) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
    Envelope transmembrane glycoprotein gp41 env HIV-1 gp41 is identified to have a physical interaction with transmembrane protein 38B (TMEM38B) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • FLJ10493

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables potassium channel activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in bone development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in bone mineralization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cellular response to caffeine IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in endoplasmic reticulum organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in establishment of localization in cell IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in extracellular matrix constituent secretion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in lung alveolus development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in lung epithelial cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phospholipid biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in potassium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in release of sequestered calcium ion into cytosol by sarcoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in secretion by lung epithelial cell involved in lung growth IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nuclear membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in nucleus HDA PubMed 
    located_in sarcoplasmic reticulum membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    trimeric intracellular cation channel type B

    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.

    Genomic

    1. NG_032971.1 RefSeqGene

      Range
      5017..87105
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_018112.3 → NP_060582.1  trimeric intracellular cation channel type B

      See identical proteins and their annotated locations for NP_060582.1

      Status: REVIEWED

      Source sequence(s)
      AK001355, AL592488, BC000049, BU728078, BX112234
      Consensus CDS
      CCDS6768.1
      UniProtKB/Swiss-Prot
      Q5JR63, Q5SVN5, Q5SVN6, Q5VTE2, Q6IA97, Q9NVV0
      Related
      ENSP00000363824.3, ENST00000374692.8
      Conserved Domains (1) summary
      pfam05197
      Location:39 → 221
      TRIC; TRIC channel

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      105694541..105776629
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011518832.4 → XP_011517134.1  trimeric intracellular cation channel type B isoform X3

      Conserved Domains (1) summary
      pfam05197
      Location:39 → 130
      TRIC; TRIC channel

    2. XM_011518831.3 → XP_011517133.1  trimeric intracellular cation channel type B isoform X2

      See identical proteins and their annotated locations for XP_011517133.1

      Conserved Domains (1) summary
      pfam05197
      Location:39 → 181
      TRIC; TRIC channel

    3. XM_005252075.3 → XP_005252132.1  trimeric intracellular cation channel type B isoform X1

      See identical proteins and their annotated locations for XP_005252132.1

      UniProtKB/TrEMBL
      A0A0A0MRS4
      Related
      ENSP00000363820.1, ENST00000374688.5
      Conserved Domains (1) summary
      pfam05197
      Location:1 → 167
      TRIC; TRIC channel

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      117869221..117951308
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363215.1 → XP_054219190.1  trimeric intracellular cation channel type B isoform X3

    2. XM_054363214.1 → XP_054219189.1  trimeric intracellular cation channel type B isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NVV0.1 GenPept UniProtKB/Swiss-Prot:Q9NVV0

    Gene LinkOut

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

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