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    TMEM39A transmembrane protein 39A [ Homo sapiens (human) ]

    Gene ID: 55254, updated on 5-Mar-2024

    Summary

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    Official Symbol
    TMEM39Aprovided by HGNC
    Official Full Name
    transmembrane protein 39Aprovided by HGNC
    Primary source
    HGNC:HGNC:25600
    See related
    Ensembl:ENSG00000176142 AllianceGenome:HGNC:25600
    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
    SUSR2
    Summary
    Involved in negative regulation of autophagosome assembly; negative regulation of autophagosome maturation; and positive regulation of viral genome replication. Located in endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in thyroid (RPKM 7.9), placenta (RPKM 6.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TMEM39A in Genome Data Viewer
    Location:
    3q13.33
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (119428949..119463615, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (122148660..122183326, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (119147796..119182462, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene Rho GTPase activating protein 31 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20299 Neighboring gene RNA, U6 small nuclear 1127, pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:119068069-119068893 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:119070415-119071112 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:119079699-119080370 Neighboring gene uncharacterized LOC124906273 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20301 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20302 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:119187474-119187974 Neighboring gene protein O-glucosyltransferase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20304 Neighboring gene MPRA-validated peak4782 silencer Neighboring gene translocase of inner mitochondrial membrane domain containing 1 Neighboring gene CD80 molecule

    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. The conserved autoimmune-disease risk gene TMEM39A regulates lysosome dynamics. Luo S, et al. Proc Natl Acad Sci U S A, 2021 Feb 9. PMID 33531362, Free PMC Article
    2. Genetic Variants in TMEM39A Gene Are Associated with Autoimmune Thyroid Diseases. Yao Q, et al. DNA Cell Biol, 2019 Nov. PMID 31553233
    3. TMEM39A and Human Diseases: A Brief Review. Tran Q, et al. Toxicol Res, 2017 Jul. PMID 28744351, Free PMC Article
    4. Preliminary Study on the Role of TMEM39A Gene in Multiple Sclerosis. Wagner M, et al. J Mol Neurosci, 2017 Jun. PMID 28444502, Free PMC Article
    5. Association of novel polymorphisms in TMEM39A gene with systemic lupus erythematosus in a Chinese Han population. Cai X, et al. BMC Med Genet, 2017 Apr 20. PMID 28427360, Free PMC Article

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Polymorphisms of the TMEM39A gene are associated with the susceptibility to Autoimmune Thyroid diseases (AITD), especially for early-onset AITD and Hashimoto thyroiditis with hypothyroidism.
      Title: Genetic Variants in TMEM39A Gene Are Associated with Autoimmune Thyroid Diseases.
    2. TMEM39A mRNA expression may be associated with the development and/or course of multiple sclerosis. rs1132200 and rs17281647 were not associated with multiple sclerosis.
      Title: Preliminary Study on the Role of TMEM39A Gene in Multiple Sclerosis.
    3. Findings identified three novel associations in SNPs located in the TMEM39A gene associated with systemic lupus erythematous susceptibility in a Chinese Han population.
      Title: Association of novel polymorphisms in TMEM39A gene with systemic lupus erythematosus in a Chinese Han population.
    4. Pooled analysis corroborated the effect on multiple sclerosis predisposition of three genes: TMEM39A, IL12B, and CBLB
      Title: Replication study of 10 genes showing evidence for association with multiple sclerosis: validation of TMEM39A, IL12B and CBLB [correction of CLBL] genes.
    5. Four additional susceptibility loci (IRF8, TMEM39A, IKZF3, and ZPBP2) for systemic lupus erythematosus were robustly established a multiethnic population (European, African American, Asian, Hispanic, Gullah, and Amerindian).
      Title: Identification of IRF8, TMEM39A, and IKZF3-ZPBP2 as susceptibility loci for systemic lupus erythematosus in a large-scale multiracial replication study.
    6. Comprehensive follow-up of the first genome-wide association study of multiple sclerosis identifies TMEM39A as susceptibility
      Title: Comprehensive follow-up of the first genome-wide association study of multiple sclerosis identifies KIF21B and TMEM39A as susceptibility loci.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.
    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
    Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
    EBI GWAS Catalog
    Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
    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

    • FLJ10902, FLJ34745

    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 autophagy IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of autophagosome assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of autophagosome assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of autophagosome maturation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of autophagosome maturation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of viral genome replication IDA
    Inferred from Direct Assay
    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 

    General protein information

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    Preferred Names
    transmembrane protein 39A
    Names
    suppressor of SQST-1 aggregates in rpl-43 mutants

    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_018266.3 → NP_060736.1  transmembrane protein 39A

      See identical proteins and their annotated locations for NP_060736.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript and encodes the functional protein.
      Source sequence(s)
      AC074271, AK001764, BC003192
      Consensus CDS
      CCDS2987.1
      UniProtKB/Swiss-Prot
      D3DN80, Q53FN4, Q53GI1, Q6PKB5, Q9NV64
      Related
      ENSP00000326063.5, ENST00000319172.10
      Conserved Domains (1) summary
      pfam10271
      Location:42 → 477
      Tmp39; Putative transmembrane protein

    RNA

    1. NR_073506.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC074271, BC003192
      Related
      ENST00000438581.6

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      119428949..119463615 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047448511.1 → XP_047304467.1  transmembrane protein 39A isoform X2

    2. XM_047448512.1 → XP_047304468.1  transmembrane protein 39A isoform X3

    3. XM_006713687.3 → XP_006713750.1  transmembrane protein 39A isoform X1

      See identical proteins and their annotated locations for XP_006713750.1

      UniProtKB/Swiss-Prot
      D3DN80, Q53FN4, Q53GI1, Q6PKB5, Q9NV64
      Conserved Domains (1) summary
      pfam10271
      Location:42 → 477
      Tmp39; Putative transmembrane protein

    4. XM_047448513.1 → XP_047304469.1  transmembrane protein 39A isoform X4

    5. XM_017006788.3 → XP_016862277.1  transmembrane protein 39A isoform X2

      Conserved Domains (1) summary
      pfam10271
      Location:42 → 449
      Tmp39; Putative transmembrane protein

    6. XM_005247578.3 → XP_005247635.1  transmembrane protein 39A isoform X3

      Conserved Domains (1) summary
      pfam10271
      Location:42 → 371
      Tmp39; Putative transmembrane protein

    7. XM_011512958.4 → XP_011511260.1  transmembrane protein 39A isoform X5

      Conserved Domains (1) summary
      pfam10271
      Location:42 → 313
      Tmp39; Putative transmembrane protein

    RNA

    1. XR_007095705.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      122148660..122183326 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054347165.1 → XP_054203140.1  transmembrane protein 39A isoform X2

    2. XM_054347167.1 → XP_054203142.1  transmembrane protein 39A isoform X3

    3. XM_054347163.1 → XP_054203138.1  transmembrane protein 39A isoform X1

      UniProtKB/Swiss-Prot
      D3DN80, Q53FN4, Q53GI1, Q6PKB5, Q9NV64

    4. XM_054347168.1 → XP_054203143.1  transmembrane protein 39A isoform X4

    5. XM_054347164.1 → XP_054203139.1  transmembrane protein 39A isoform X2

    6. XM_054347166.1 → XP_054203141.1  transmembrane protein 39A isoform X3

    7. XM_054347169.1 → XP_054203144.1  transmembrane protein 39A isoform X5

    RNA

    1. XR_008486747.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NV64.1 GenPept UniProtKB/Swiss-Prot:Q9NV64

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