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    TMEM260 transmembrane protein 260 [ Homo sapiens (human) ]

    Gene ID: 54916, updated on 2-Nov-2024

    Summary

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    Official Symbol
    TMEM260provided by HGNC
    Official Full Name
    transmembrane protein 260provided by HGNC
    Primary source
    HGNC:HGNC:20185
    See related
    Ensembl:ENSG00000070269 MIM:617449; AllianceGenome:HGNC:20185
    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
    SHDRA; C14orf101
    Summary
    Enables dolichyl-phosphate-mannose-protein mannosyltransferase activity. Involved in protein maturation. Is active in endoplasmic reticulum membrane. Implicated in T-cell non-Hodgkin lymphoma; non-Hodgkin lymphoma; and stomach cancer. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 3.9), ovary (RPKM 3.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TMEM260 in Genome Data Viewer
    Location:
    14q22.3
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (56579525..56663165)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (50785268..50870723)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (57046516..57116233)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2284 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:56880383-56881582 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:56913685-56914290 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:56914291-56914896 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:56919397-56919898 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:56919899-56920398 Neighboring gene uncharacterized LOC101927690 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34259 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34268 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34274 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:56991474-56992081 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34296 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34318 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:57028256-57028447 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5790 Neighboring gene NANOG hESC enhancer GRCh37_chr14:57115102-57115779 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:57132632-57133831 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_34331 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:57154864-57155025 Neighboring gene uncharacterized LOC124903433 Neighboring gene ribosomal protein L36a 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 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 c.1617del variant of TMEM260 is identified as the most frequent single gene determinant for Japanese patients with a specific type of congenital heart disease. Inoue T, et al. J Hum Genet, 2024 May. PMID 38409496, Free PMC Article
    2. Genetic etiology of truncus arteriosus excluding 22q11.2 deletion syndrome and identification of c.1617del, a prevalent variant in TMEM260, in the Japanese population. Yaoita H, et al. J Hum Genet, 2024 May. PMID 38351237, Free PMC Article
    3. Biallelic TMEM260 variants cause truncus arteriosus, with or without renal defects. Pagnamenta AT, et al. Clin Genet, 2022 Jan. PMID 34612517
    4. Mutations in TMEM260 Cause a Pediatric Neurodevelopmental, Cardiac, and Renal Syndrome. Ta-Shma A, et al. Am J Hum Genet, 2017 Apr 6. PMID 28318500, Free PMC Article
    5. A polymorphism at the microRNA binding site in the 3' untranslated region of C14orf101 is associated with non-Hodgkin lymphoma overall survival. Yang B, et al. Cancer Genet, 2014 Apr. PMID 24831772

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The c.1617del variant of TMEM260 is identified as the most frequent single gene determinant for Japanese patients with a specific type of congenital heart disease.
      Title: The c.1617del variant of TMEM260 is identified as the most frequent single gene determinant for Japanese patients with a specific type of congenital heart disease.
    2. Genetic etiology of truncus arteriosus excluding 22q11.2 deletion syndrome and identification of c.1617del, a prevalent variant in TMEM260, in the Japanese population.
      Title: Genetic etiology of truncus arteriosus excluding 22q11.2 deletion syndrome and identification of c.1617del, a prevalent variant in TMEM260, in the Japanese population.
    3. The SHDRA syndrome-associated gene TMEM260 encodes a protein-specific O-mannosyltransferase.
      Title: The SHDRA syndrome-associated gene TMEM260 encodes a protein-specific O-mannosyltransferase.
    4. Biallelic TMEM260 variants cause truncus arteriosus, with or without renal defects.
      Title: Biallelic TMEM260 variants cause truncus arteriosus, with or without renal defects.
    5. Study showed that truncating mutations in TMEM260 cause a syndrome characterized by central nervous sustem, cardiac, renal, and axial skeletal defects. Notably, the homozygous truncating mutations found in the two families affected specifically one of the two splice isoforms generated by this locus, arguing specificity in the phenotypic driver.
      Title: Mutations in TMEM260 Cause a Pediatric Neurodevelopmental, Cardiac, and Renal Syndrome.
    6. Data indicate that rs4901706, located in the 3' UTR of C14orf101, was shown to be independently related to overall survival in non-Hodgkin lymphoma (NHL).
      Title: A polymorphism at the microRNA binding site in the 3' untranslated region of C14orf101 is associated with non-Hodgkin lymphoma overall survival.
    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

    Associated conditions

    Description Tests
    Structural heart defects and renal anomalies syndrome
    MedGen: C4479549 OMIM: 617478 GeneReviews: Not available
    		not available

    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

    • FLJ20392

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables dolichyl-phosphate-mannose-protein mannosyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein O-linked mannosylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein maturation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein O-mannosyl-transferase TMEM260
    Names
    UPF0679 protein C14orf101
    NP_060269.3
    XP_011535153.1
    XP_011535154.1
    XP_047287449.1
    XP_047287450.1
    XP_047287451.1
    XP_047287452.1
    XP_047287453.1
    XP_047287454.1
    XP_054232221.1
    XP_054232222.1
    XP_054232223.1
    XP_054232224.1
    XP_054232225.1
    XP_054232226.1
    XP_054232227.1
    XP_054232228.1

    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_017799.4 → NP_060269.3  protein O-mannosyl-transferase TMEM260 precursor

      See identical proteins and their annotated locations for NP_060269.3

      Status: VALIDATED

      Source sequence(s)
      AK023885, AK056291, AL161757, BX647387
      Consensus CDS
      CCDS9727.2
      UniProtKB/Swiss-Prot
      A8KAN4, B3KPF5, Q0VAA1, Q86XE1, Q9NX78
      UniProtKB/TrEMBL
      Q0IJ48
      Related
      ENSP00000261556.6, ENST00000261556.11
      Conserved Domains (1) summary
      pfam11028
      Location:52 → 206
      DUF2723; Protein of unknown function (DUF2723)

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      56579525..56663165
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047431494.1 → XP_047287450.1  protein O-mannosyl-transferase TMEM260 isoform X3

    2. XM_011536851.3 → XP_011535153.1  protein O-mannosyl-transferase TMEM260 isoform X1

      UniProtKB/TrEMBL
      Q0IJ48
      Conserved Domains (1) summary
      pfam11028
      Location:52 → 206
      DUF2723; Protein of unknown function (DUF2723)

    3. XM_047431497.1 → XP_047287453.1  protein O-mannosyl-transferase TMEM260 isoform X6

      Related
      ENSP00000441934.1, ENST00000538838.5

    4. XM_047431495.1 → XP_047287451.1  protein O-mannosyl-transferase TMEM260 isoform X4

    5. XM_047431496.1 → XP_047287452.1  protein O-mannosyl-transferase TMEM260 isoform X5

    6. XM_047431493.1 → XP_047287449.1  protein O-mannosyl-transferase TMEM260 isoform X3

    7. XM_011536852.2 → XP_011535154.1  protein O-mannosyl-transferase TMEM260 isoform X2

    8. XM_047431498.1 → XP_047287454.1  protein O-mannosyl-transferase TMEM260 isoform X7

    RNA

    1. XR_007064017.1 RNA Sequence

    2. XR_007064018.1 RNA Sequence

    3. XR_007064019.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      50785268..50870723
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054376249.1 → XP_054232224.1  protein O-mannosyl-transferase TMEM260 isoform X3

    2. XM_054376246.1 → XP_054232221.1  protein O-mannosyl-transferase TMEM260 isoform X1

    3. XM_054376252.1 → XP_054232227.1  protein O-mannosyl-transferase TMEM260 isoform X6

    4. XM_054376250.1 → XP_054232225.1  protein O-mannosyl-transferase TMEM260 isoform X4

    5. XM_054376251.1 → XP_054232226.1  protein O-mannosyl-transferase TMEM260 isoform X5

    6. XM_054376248.1 → XP_054232223.1  protein O-mannosyl-transferase TMEM260 isoform X3

    7. XM_054376247.1 → XP_054232222.1  protein O-mannosyl-transferase TMEM260 isoform X2

    8. XM_054376253.1 → XP_054232228.1  protein O-mannosyl-transferase TMEM260 isoform X7

    RNA

    1. XR_008488876.1 RNA Sequence

    2. XR_008488877.1 RNA Sequence

    3. XR_008488878.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NX78.3 GenPept UniProtKB/Swiss-Prot:Q9NX78

    Gene LinkOut

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