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    TMEM178A transmembrane protein 178A [ Homo sapiens (human) ]

    Gene ID: 130733, updated on 30-Oct-2024

    Summary

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    Official Symbol
    TMEM178Aprovided by HGNC
    Official Full Name
    transmembrane protein 178Aprovided by HGNC
    Primary source
    HGNC:HGNC:28517
    See related
    Ensembl:ENSG00000152154 AllianceGenome:HGNC:28517
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    TMEM178
    Summary
    Predicted to be involved in negative regulation of osteoclast differentiation and regulation of cytosolic calcium ion concentration. Predicted to be located in endoplasmic reticulum and membrane. Predicted to be active in endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Biased expression in brain (RPKM 5.0), prostate (RPKM 2.7) and 11 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TMEM178A in Genome Data Viewer
    Location:
    2p22.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (39665483..39735960)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (39673667..39744956)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (39892623..39945103)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene mitogen-activated protein kinase kinase kinase kinase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15616 Neighboring gene RNA, U6 small nuclear 1341, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15617 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11386 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11387 Neighboring gene MAP4K3 divergent transcript Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:39696648-39697148 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11388 Neighboring gene Sharpr-MPRA regulatory region 10578 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:39742467-39742687 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:39742776-39743368 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:39743369-39743960 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:39743961-39744553 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15618 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:39948161-39948662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:39948663-39949162 Neighboring gene uncharacterized LOC124905994 Neighboring gene NANOG hESC enhancer GRCh37_chr2:39999086-40000066 Neighboring gene THUMP domain containing 2 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:40016715-40017914 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:40065678-40066225 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15619 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:40128919-40130118 Neighboring gene uncharacterized LOC112268436

    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. Refining the role of de novo protein-truncating variants in neurodevelopmental disorders by using population reference samples. Kosmicki JA, et al. Nat Genet, 2017 Apr. PMID 28191890, Free PMC Article
    2. Tmem178 acts in a novel negative feedback loop targeting NFATc1 to regulate bone mass. Decker CE, et al. Proc Natl Acad Sci U S A, 2015 Dec 22. PMID 26644563, Free PMC Article
    3. Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. Otsuki T, et al. DNA Res, 2005. PMID 16303743
    4. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. Comuzzie AG, et al. PLoS One, 2012. PMID 23251661, Free PMC Article
    5. Sequential genome-wide CRISPR-Cas9 screens identify genes regulating cell-surface expression of tetraspanins. Yang J, et al. Cell Rep, 2023 Feb 28. PMID 36724073

    See all (11) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Tmem178 localizes to the ER membrane and regulates RANKL-induced Ca(2+) fluxes, thus controlling NFATc1 induction
      Title: Tmem178 acts in a novel negative feedback loop targeting NFATc1 to regulate bone mass.
    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

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2024-10-23)

    ClinGen Genome Curation Page
    Haploinsufficency

    No evidence available (Last evaluated 2024-10-23)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC33926

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in negative regulation of osteoclast differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of osteoclast differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of cytosolic calcium ion concentration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of cytosolic calcium ion concentration ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    transmembrane protein 178A
    Names
    transmembrane protein 178

    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_001167959.2 → NP_001161431.1  transmembrane protein 178A isoform 2

      See identical proteins and their annotated locations for NP_001161431.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains a distinct 5' UTR and lacks an in-frame portion of the 5' coding region, compared to variant 1. The resulting isoform (2) has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC007246, BC029530, BI757636
      UniProtKB/Swiss-Prot
      Q8NBL3
      Conserved Domains (1) summary
      cl21598
      Location:2 → 92
      PMP22_Claudin; PMP-22/EMP/MP20/Claudin family

    2. NM_152390.3 → NP_689603.2  transmembrane protein 178A isoform 1 precursor

      See identical proteins and their annotated locations for NP_689603.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC007246, BC029530, DN993805
      Consensus CDS
      CCDS1804.1
      UniProtKB/Swiss-Prot
      Q6UWI6, Q8N6N4, Q8NBL3
      Related
      ENSP00000281961.2, ENST00000281961.3
      Conserved Domains (1) summary
      cl21598
      Location:106 → 274
      PMP22_Claudin; PMP-22/EMP/MP20/Claudin family

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      39665483..39735960
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024452702.2 → XP_024308470.1  transmembrane protein 178A isoform X4

    2. XM_005264144.1 → XP_005264201.1  transmembrane protein 178A isoform X1

      See identical proteins and their annotated locations for XP_005264201.1

    3. XM_005264145.1 → XP_005264202.1  transmembrane protein 178A isoform X3

      Conserved Domains (1) summary
      cl21598
      Location:28 → 190
      PMP22_Claudin; PMP-22/EMP/MP20/Claudin family

    4. XM_017003369.2 → XP_016858858.1  transmembrane protein 178A isoform X2

    5. XM_047443422.1 → XP_047299378.1  transmembrane protein 178A isoform X5

    6. XM_017003371.2 → XP_016858860.1  transmembrane protein 178A isoform X5

      Conserved Domains (1) summary
      cl21598
      Location:2 → 92
      PMP22_Claudin; PMP-22/EMP/MP20/Claudin family

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      39673667..39744956
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054340584.1 → XP_054196559.1  transmembrane protein 178A isoform X5

    2. XM_054340585.1 → XP_054196560.1  transmembrane protein 178A isoform X5

    3. XM_054340582.1 → XP_054196557.1  transmembrane protein 178A isoform X5

    4. XM_054340581.1 → XP_054196556.1  transmembrane protein 178A isoform X4

    5. XM_054340578.1 → XP_054196553.1  transmembrane protein 178A isoform X1

    6. XM_054340580.1 → XP_054196555.1  transmembrane protein 178A isoform X3

    7. XM_054340579.1 → XP_054196554.1  transmembrane protein 178A isoform X2

    8. XM_054340586.1 → XP_054196561.1  transmembrane protein 178A isoform X5

    9. XM_054340583.1 → XP_054196558.1  transmembrane protein 178A isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NBL3.1 GenPept UniProtKB/Swiss-Prot:Q8NBL3

    Gene LinkOut

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

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