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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
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Genomic context

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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

Gene LinkOut

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