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

Gene ID: 55151, updated on 3-Nov-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
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Genomic context

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See TMEM38B in Genome Data Viewer
Location:
9q31.2
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (105694541..105776629)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (117869221..117951308)
RS_2024_09 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 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. A deletion mutation in TMEM38B associated with autosomal recessive osteogenesis imperfecta. Volodarsky M, et al. Hum Mutat, 2013 Apr. PMID 23316006
  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. 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
  4. Absence of TRIC-B from type XIV Osteogenesis Imperfecta osteoblasts alters cell adhesion and mitochondrial function - A multi-omics study. Jovanovic M, et al. Matrix Biol, 2023 Aug. PMID 37348683, Free PMC Article
  5. 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

See all (44) 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 ISS
Inferred from Sequence or Structural Similarity
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 regulation of release of sequestered calcium ion into cytosol ISS
Inferred from Sequence or Structural Similarity
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 endoplasmic reticulum ISS
Inferred from Sequence or Structural Similarity
more info
  
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_2024_08

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

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