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    TMEM170A transmembrane protein 170A [ Homo sapiens (human) ]

    Gene ID: 124491, updated on 27-Nov-2024

    Summary

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    Official Symbol
    TMEM170Aprovided by HGNC
    Official Full Name
    transmembrane protein 170Aprovided by HGNC
    Primary source
    HGNC:HGNC:29577
    See related
    Ensembl:ENSG00000166822 MIM:620630; AllianceGenome:HGNC:29577
    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
    TMEM170
    Summary
    Involved in endoplasmic reticulum tubular network organization; nuclear envelope organization; and nuclear pore complex assembly. Located in endoplasmic reticulum membrane and nuclear envelope. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in colon (RPKM 6.4), duodenum (RPKM 5.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TMEM170A in Genome Data Viewer
    Location:
    16q23.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (75443054..75464737, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (81488941..81510632, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (75476952..75498635, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene craniofacial development protein 1 Neighboring gene small nucleolar RNA SNORA76 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:75465381-75465580 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7719 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75467440-75468007 Neighboring gene tigger transposable element-derived protein 1-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:75490353-75490854 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11131 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:75498257-75498757 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:75505547-75506189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11133 Neighboring gene carbohydrate sulfotransferase 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11134 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7721 Neighboring gene TMEM231 pseudogene 1

    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. Identification of the BCAR1-CFDP1-TMEM170A locus as a determinant of carotid intima-media thickness and coronary artery disease risk. Gertow K, et al. Circ Cardiovasc Genet, 2012 Dec. PMID 23152477
    2. Transmembrane protein TMEM170A is a newly discovered regulator of ER and nuclear envelope morphogenesis in human cells. Christodoulou A, et al. J Cell Sci, 2016 Apr 15. PMID 26906412, Free PMC Article
    3. Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects. Dastani Z, et al. Eur J Hum Genet, 2010 Mar. PMID 19844255, Free PMC Article
    4. Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer. Wolpin BM, et al. Nat Genet, 2014 Sep. PMID 25086665, Free PMC Article
    5. N(6)-Methyladenosine on mRNA facilitates a phase-separated nuclear body that suppresses myeloid leukemic differentiation. Cheng Y, et al. Cancer Cell, 2021 Jul 12. PMID 34048709, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. this paper shows that that downregulation of TMEM170A specifically induces tubular endoplasmic reticulum formation, whereas overexpression of TMEM170A induces endoplasmic reticulum sheet formation.
      Title: Transmembrane protein TMEM170A is a newly discovered regulator of ER and nuclear envelope morphogenesis in human cells.
    2. This study identified rs4888378 in the BCAR1-CFDP1-TMEM170A locus as a novel genetic determinant of carotid intima-media thickness and coronary artery disease risk.
      Title: Identification of the BCAR1-CFDP1-TMEM170A locus as a determinant of carotid intima-media thickness and coronary artery disease risk.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies multiple susceptibility loci for pancreatic cancer.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ37611

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endoplasmic reticulum tubular network organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endoplasmic reticulum tubular network organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nuclear envelope organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nuclear pore complex assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear envelope IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    transmembrane protein 170A
    Names
    transmembrane protein 170

    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_001304996.2 → NP_001291925.1  transmembrane protein 170A isoform 2

      See identical proteins and their annotated locations for NP_001291925.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. The encoded isoform (2) is shorter compared to isoform 1.
      Source sequence(s)
      AC009163, AK298475
      Consensus CDS
      CCDS76901.1
      UniProtKB/Swiss-Prot
      Q8WVE7
      Related
      ENSP00000350230.4, ENST00000357613.8
      Conserved Domains (1) summary
      pfam10190
      Location:42 → 117
      Tmemb_170; Putative transmembrane protein 170

    2. NM_001304997.2 → NP_001291926.1  transmembrane protein 170A isoform 3

      See identical proteins and their annotated locations for NP_001291926.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate 5'-terminal exon and an alternate start codon compared to variant 1. The encoded isoform (3) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC009163, AK094930
      Consensus CDS
      CCDS76900.1
      UniProtKB/TrEMBL
      B3KT46
      Related
      ENSP00000455491.1, ENST00000569540.5
      Conserved Domains (1) summary
      pfam10190
      Location:7 → 102
      Tmemb_170; Putative transmembrane protein 170

    3. NM_001304998.1 → NP_001291927.1  transmembrane protein 170A isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks part of the 5' coding region, uses an alternate splice site in the 3' coding region, and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (4) is shorter compared to isoform 1.
      Source sequence(s)
      AC009163, DA370427
      Consensus CDS
      CCDS76899.1
      UniProtKB/TrEMBL
      H3BRD7
      Related
      ENSP00000456194.1, ENST00000566980.1
      Conserved Domains (1) summary
      pfam10190
      Location:1 → 72
      Tmemb_170; Putative transmembrane protein 170

    4. NM_145254.3 → NP_660297.1  transmembrane protein 170A isoform 1

      See identical proteins and their annotated locations for NP_660297.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC009163, AK311919
      Consensus CDS
      CCDS10917.1
      UniProtKB/Swiss-Prot
      B2R4R3, B4DPS4, D3DUK2, Q7Z6F3, Q8WVE7
      Related
      ENSP00000454404.1, ENST00000561878.2
      Conserved Domains (1) summary
      pfam10190
      Location:39 → 144
      Tmemb_170; Putative transmembrane protein 170

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      75443054..75464737 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017022941.2 → XP_016878430.1  transmembrane protein 170A isoform X4

      UniProtKB/TrEMBL
      H3BS26
      Related
      ENSP00000456509.1, ENST00000567796.1

    2. XM_017022943.2 → XP_016878432.1  transmembrane protein 170A isoform X6

    3. XM_017022940.2 → XP_016878429.1  transmembrane protein 170A isoform X3

    4. XM_011522869.3 → XP_011521171.1  transmembrane protein 170A isoform X1

      Conserved Domains (1) summary
      pfam10190
      Location:36 → 131
      Tmemb_170; Putative transmembrane protein 170

    5. XM_017022942.2 → XP_016878431.1  transmembrane protein 170A isoform X5

    6. XM_017022939.2 → XP_016878428.1  transmembrane protein 170A isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      81488941..81510632 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054379617.1 → XP_054235592.1  transmembrane protein 170A isoform X4

    2. XM_054379613.1 → XP_054235588.1  transmembrane protein 170A isoform X6

    3. XM_054379616.1 → XP_054235591.1  transmembrane protein 170A isoform X3

    4. XM_054379614.1 → XP_054235589.1  transmembrane protein 170A isoform X1

    5. XM_054379618.1 → XP_054235593.1  transmembrane protein 170A isoform X5

    6. XM_054379615.1 → XP_054235590.1  transmembrane protein 170A isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WVE7.1 GenPept UniProtKB/Swiss-Prot:Q8WVE7

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