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] See more...

Aliases for TMEM38B Gene

Aliases for TMEM38B Gene

  • Transmembrane Protein 38B 2 3 4 5
  • Trimeric Intracellular Cation Channel Type B 3 4
  • C9orf87 3 4
  • TRIC-B 3 4
  • TRICB 3 4
  • Chromosome 9 Open Reading Frame 87 2
  • BA219P18.1 3
  • D4Ertd89e 3
  • OI14 3

External Ids for TMEM38B Gene

Previous HGNC Symbols for TMEM38B Gene

  • C9orf87

Previous GeneCards Identifiers for TMEM38B Gene

  • GC09P105537
  • GC09P107497
  • GC09P108456
  • GC09P078058

Summaries for TMEM38B Gene

Entrez Gene Summary for TMEM38B Gene

  • 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]

GeneCards Summary for TMEM38B Gene

TMEM38B (Transmembrane Protein 38B) is a Protein Coding gene. Diseases associated with TMEM38B include Osteogenesis Imperfecta, Type Xiv and Osteogenesis Imperfecta, Type Iv. Gene Ontology (GO) annotations related to this gene include potassium channel activity and cation channel activity. An important paralog of this gene is TMEM38A.

UniProtKB/Swiss-Prot Summary for TMEM38B Gene

  • Monovalent cation channel required for maintenance of rapid intracellular calcium release. May act as a potassium counter-ion channel that functions in synchronization with calcium release from intracellular stores.

Additional gene information for TMEM38B Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for TMEM38B Gene

Genomics for TMEM38B Gene

GeneHancer (GH) Regulatory Elements for TMEM38B Gene

Promoters and enhancers for TMEM38B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J105693 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 524 +0.4 376 3.8 ZNF217 ZSCAN5C NRF1 POLR2G USF1 ZFX POLR2A ZNF263 AFF1 ZBTB26 TMEM38B lnc-ABCA1-11 lnc-TAL2-2
GH09J105656 Promoter 1.7 EPDnew Ensembl CraniofacialAtlas 507.6 -38.1 -38065 1.5 CTCF REST KLF4 CTBP1 EZH2 HDAC2 MYC KDM5B RBM14 SMC3 TMEM38B ENSG00000279609 lnc-ABCA1-7 lnc-TAL2-1 lnc-TAL2-2 ENSG00000228366 TAL2
GH09J105700 Enhancer 0.8 Ensembl ENCODE 23.9 +6.1 6096 2.8 RBM25 CEBPG CEBPB TRIM28 BCOR MNT ZNF189 PRDM6 ZMYM3 MAX TMEM38B piR-61514-208 lnc-ABCA1-11 lnc-TAL2-2
GH09J105646 Enhancer 1.1 Ensembl ENCODE 11.1 -47.1 -47129 2 PHB2 ZBTB11 AFF1 TRIM28 TARDBP REST HES1 MYC CTBP1 JUN TMEM38B FKTN FSD1L lnc-ABCA1-7 lnc-ABCA1-6
GH09J105288 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 6.8 -400.0 -400024 13 EP300 ZNF217 TCF12 NCOR1 JUND FOS KDM6A CLOCK TCF7 ZBTB25 SLC44A1 ABCA1 FSD1L TMEM38B RF00998-138 NONHSAG053105.2 lnc-FSD1L-1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around TMEM38B on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for TMEM38B

Top Transcription factor binding sites by QIAGEN in the TMEM38B gene promoter:
  • C/EBPalpha
  • FOXJ2
  • FOXJ2 (long isoform)
  • Oct-B1
  • oct-B2
  • oct-B3
  • POU2F1
  • POU2F1a
  • POU2F2
  • POU2F2 (Oct-2.1)

Genomic Locations for TMEM38B Gene

Genomic Locations for TMEM38B Gene
chr9:105,694,525-105,776,629
(GRCh38/hg38)
Size:
82,105 bases
Orientation:
Plus strand
chr9:108,456,825-108,538,893
(GRCh37/hg19)
Size:
82,069 bases
Orientation:
Plus strand

Genomic View for TMEM38B Gene

Genes around TMEM38B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TMEM38B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TMEM38B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TMEM38B Gene

Proteins for TMEM38B Gene

  • Protein details for TMEM38B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NVV0-TM38B_HUMAN
    Recommended name:
    Trimeric intracellular cation channel type B
    Protein Accession:
    Q9NVV0
    Secondary Accessions:
    • Q5JR63
    • Q5SVN5
    • Q5SVN6
    • Q5VTE2
    • Q6IA97

    Protein attributes for TMEM38B Gene

    Size:
    291 amino acids
    Molecular mass:
    32510 Da
    Quaternary structure:
    • Homotrimer; trimerization probably requires binding to phosphatidylinositol 4,5-bisphosphate (PIP2).

neXtProt entry for TMEM38B Gene

Post-translational modifications for TMEM38B Gene

  • Ubiquitination at Lys166
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for TMEM38B Gene

Domains & Families for TMEM38B Gene

Gene Families for TMEM38B Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Potential drug targets
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transporters

Protein Domains for TMEM38B Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for TMEM38B Gene

GenScript: Design optimal peptide antigens:
  • Transmembrane protein 38B (TM38B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NVV0

UniProtKB/Swiss-Prot:

TM38B_HUMAN :
  • Belongs to the TMEM38 family.
Family:
  • Belongs to the TMEM38 family.
genes like me logo Genes that share domains with TMEM38B: view

Function for TMEM38B Gene

Molecular function for TMEM38B Gene

UniProtKB/Swiss-Prot Function:
Monovalent cation channel required for maintenance of rapid intracellular calcium release. May act as a potassium counter-ion channel that functions in synchronization with calcium release from intracellular stores.

Phenotypes From GWAS Catalog for TMEM38B Gene

Gene Ontology (GO) - Molecular Function for TMEM38B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005261 cation channel activity IEA --
GO:0005267 potassium channel activity TAS 19095005
genes like me logo Genes that share ontologies with TMEM38B: view
genes like me logo Genes that share phenotypes with TMEM38B: view

Human Phenotype Ontology for TMEM38B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for TMEM38B Gene

MGI Knock Outs for TMEM38B:

Animal Model Products

  • Taconic Biosciences Mouse Models for TMEM38B

CRISPR Products

miRNA for TMEM38B Gene

miRTarBase miRNAs that target TMEM38B

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TMEM38B

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for TMEM38B Gene

Localization for TMEM38B Gene

Subcellular locations from UniProtKB/Swiss-Prot for TMEM38B Gene

Endoplasmic reticulum membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TMEM38B gene
Compartment Confidence
nucleus 4
endoplasmic reticulum 4
plasma membrane 2
extracellular 1
cytosol 1
peroxisome 0
lysosome 0

Gene Ontology (GO) - Cellular Components for TMEM38B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005623 cell IEA --
GO:0005634 nucleus HDA 21630459
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with TMEM38B: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for TMEM38B Gene

Pathways & Interactions for TMEM38B Gene

PathCards logo

SuperPathways for TMEM38B Gene

No Data Available

Interacting Proteins for TMEM38B Gene

;

Gene Ontology (GO) - Biological Process for TMEM38B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0006813 potassium ion transport IEA --
GO:0007029 endoplasmic reticulum organization IEA --
GO:0008654 phospholipid biosynthetic process IEA --
GO:0010881 regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion IEA --
genes like me logo Genes that share ontologies with TMEM38B: view

No data available for Pathways by source and SIGNOR curated interactions for TMEM38B Gene

Drugs & Compounds for TMEM38B Gene

(1) Drugs for TMEM38B Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Approved Nutra 7884
genes like me logo Genes that share compounds with TMEM38B: view

Transcripts for TMEM38B Gene

mRNA/cDNA for TMEM38B Gene

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for TMEM38B

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TMEM38B Gene

No ASD Table

Relevant External Links for TMEM38B Gene

GeneLoc Exon Structure for
TMEM38B

Expression for TMEM38B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TMEM38B Gene

mRNA differential expression in normal tissues according to GTEx for TMEM38B Gene

This gene is overexpressed in Muscle - Skeletal (x7.8).

Protein differential expression in normal tissues from HIPED for TMEM38B Gene

This gene is overexpressed in Testis (22.2), Islet of Langerhans (11.5), Fetal gut (8.4), and Kidney (7.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for TMEM38B Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for TMEM38B

SOURCE GeneReport for Unigene cluster for TMEM38B Gene:

Hs.411925

Evidence on tissue expression from TISSUES for TMEM38B Gene

  • Kidney(4.3)
  • Nervous system(3.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for TMEM38B Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cheek
  • chin
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • middle ear
  • mouth
  • neck
  • nose
  • skull
  • tooth
Thorax:
  • chest wall
  • clavicle
  • heart
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • biliary tract
  • kidney
  • liver
Pelvis:
  • pelvis
  • ureter
  • uterus
  • vagina
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with TMEM38B: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for TMEM38B Gene

Orthologs for TMEM38B Gene

This gene was present in the common ancestor of animals.

Orthologs for TMEM38B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TMEM38B 31 30
  • 99.77 (n)
OneToOne
dog
(Canis familiaris)
Mammalia TMEM38B 31 30
  • 88.93 (n)
OneToOne
cow
(Bos Taurus)
Mammalia TMEM38B 31 30
  • 87.86 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Tmem38b 30
  • 80.69 (n)
mouse
(Mus musculus)
Mammalia Tmem38b 17 31 30
  • 80.57 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia TMEM38B 31
  • 60 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia TMEM38B 31
  • 52 (a)
OneToOne
chicken
(Gallus gallus)
Aves TMEM38B 31 30
  • 67.14 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia TMEM38B 31
  • 57 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tmem38b 30
  • 60.5 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.15857 30
zebrafish
(Danio rerio)
Actinopterygii tmem38b 30
  • 53.41 (n)
CABZ01079427.1 31
  • 39 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG4239 31
  • 33 (a)
ManyToMany
CG33061 31
  • 22 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea Y57A10A.10 31
  • 28 (a)
ManyToMany
Y57A10A.28 31
  • 28 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8498 31
  • 27 (a)
OneToMany
Species where no ortholog for TMEM38B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for TMEM38B Gene

ENSEMBL:
Gene Tree for TMEM38B (if available)
TreeFam:
Gene Tree for TMEM38B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for TMEM38B: view image

Paralogs for TMEM38B Gene

Paralogs for TMEM38B Gene

(1) SIMAP similar genes for TMEM38B Gene using alignment to 3 proteins:

  • TM38B_HUMAN
  • H7C3B3_HUMAN
  • H7C4C1_HUMAN

Pseudogenes.org Pseudogenes for TMEM38B Gene

genes like me logo Genes that share paralogs with TMEM38B: view

Variants for TMEM38B Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for TMEM38B Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
669656 Likely Benign: not provided 105,695,074(+) G/A INTRON_VARIANT
669658 Benign: not provided 105,705,326(+) A/G INTRON_VARIANT
669660 Benign: not provided 105,721,308(+) G/A INTRON_VARIANT
674963 Benign: not provided 105,705,848(+) C/T INTRON_VARIANT
708103 Benign: not provided 105,774,003(+) G/A MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for TMEM38B Gene

Structural Variations from Database of Genomic Variants (DGV) for TMEM38B Gene

Variant ID Type Subtype PubMed ID
dgv12837n54 CNV loss 21841781
dgv12838n54 CNV loss 21841781
dgv12839n54 CNV gain+loss 21841781
dgv12840n54 CNV gain 21841781
dgv12841n54 CNV gain+loss 21841781
dgv12842n54 CNV gain 21841781
dgv12843n54 CNV gain 21841781
dgv1369e199 CNV deletion 23128226
dgv7698n100 CNV loss 25217958
esv2666375 CNV deletion 23128226
esv2670351 CNV deletion 23128226
esv2675392 CNV deletion 23128226
esv26979 CNV gain 19812545
esv2738883 CNV deletion 23290073
esv3545255 CNV deletion 23714750
esv3621361 CNV loss 21293372
esv3621363 CNV loss 21293372
esv3621364 CNV gain 21293372
esv3621365 CNV loss 21293372
esv3891705 CNV loss 25118596
esv3891707 CNV gain 25118596
nsv1115217 CNV deletion 24896259
nsv1117521 CNV tandem duplication 24896259
nsv508558 CNV deletion 20534489
nsv615116 CNV loss 21841781
nsv615117 CNV loss 21841781
nsv615127 CNV loss 21841781
nsv615138 CNV loss 21841781
nsv615139 CNV loss 21841781
nsv6653 CNV insertion 18451855
nsv825027 CNV gain 20364138
nsv968742 CNV duplication 23825009
nsv982335 CNV duplication 23825009

Variation tolerance for TMEM38B Gene

Residual Variation Intolerance Score: 58.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.84; 17.57% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for TMEM38B Gene

Human Gene Mutation Database (HGMD)
TMEM38B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TMEM38B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TMEM38B Gene

Disorders for TMEM38B Gene

MalaCards: The human disease database

(7) MalaCards diseases for TMEM38B Gene - From: OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
osteogenesis imperfecta, type xiv
  • oi14
osteogenesis imperfecta, type iv
  • oi4
dentinogenesis imperfecta
  • di
cole-carpenter syndrome
  • bone fragility with craniosynostosis, ocular proptosis, hydrocephalus, and distinctive facial features
bruck syndrome
  • osteogenesis imperfecta with congenital joint contractures
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

TM38B_HUMAN
  • Osteogenesis imperfecta 14 (OI14) [MIM:615066]: An autosomal recessive form of osteogenesis imperfecta, a connective tissue disorder characterized by low bone mass, bone fragility and susceptibility to fractures after minimal trauma. Disease severity ranges from very mild forms without fractures to intrauterine fractures and perinatal lethality. Extraskeletal manifestations, which affect a variable number of patients, are dentinogenesis imperfecta, hearing loss, and blue sclerae. OI14 is characterized by variable degrees of severity of multiple fractures and osteopenia, with normal teeth, sclerae, and hearing. Fractures first occur prenatally or by age 6 years. {ECO:0000269 PubMed:23054245, ECO:0000269 PubMed:23316006}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for TMEM38B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with TMEM38B: view

No data available for Genatlas for TMEM38B Gene

Publications for TMEM38B Gene

  1. A deletion mutation in TMEM38B associated with autosomal recessive osteogenesis imperfecta. (PMID: 23316006) Volodarsky M … Birk OS (Human mutation 2013) 2 3 4 54
  2. Study of autosomal recessive osteogenesis imperfecta in Arabia reveals a novel locus defined by TMEM38B mutation. (PMID: 23054245) Shaheen R … Alkuraya FS (Journal of medical genetics 2012) 3 4 54
  3. Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study. (PMID: 20800603) Flachsbart F … Nebel A (Mutation research 2010) 3 41 54
  4. Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies. (PMID: 21102462) Elks CE … Murray A (Nature genetics 2010) 3 41 54
  5. Meta-analysis of genome-wide association data identifies two loci influencing age at menarche. (PMID: 19448620) Perry JR … Murabito JM (Nature genetics 2009) 3 41 54

Products for TMEM38B Gene

Sources for TMEM38B Gene