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    THUMPD1 THUMP domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 55623, updated on 5-May-2024

    Summary

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    Official Symbol
    THUMPD1provided by HGNC
    Official Full Name
    THUMP domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:23807
    See related
    Ensembl:ENSG00000066654 MIM:616662; AllianceGenome:HGNC:23807
    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
    Tan1; NEDSOA
    Summary
    Enables RNA binding activity. Predicted to be involved in tRNA modification. Predicted to be located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in prostate (RPKM 15.3), endometrium (RPKM 11.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See THUMPD1 in Genome Data Viewer
    Location:
    16p12.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (20733664..20741818, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (20664595..20672749, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (20744986..20753140, complement)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene acyl-CoA synthetase medium chain family member 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:20658967-20659531 Neighboring gene NANOG hESC enhancer GRCh37_chr16:20662170-20662773 Neighboring gene NANOG hESC enhancer GRCh37_chr16:20693644-20694145 Neighboring gene acyl-CoA synthetase medium chain family member 3 Neighboring gene NADH-ubiquinone oxidoreductase chain 5-like Neighboring gene acyl-CoA synthetase medium chain family member 4 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10536 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10535 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10537 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10538 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10539 Neighboring gene RNA, U6 small nuclear 944, pseudogene Neighboring gene ERI1 exoribonuclease family member 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:20816990-20817935 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10541 Neighboring gene RNA exonuclease 5 Neighboring gene uncharacterized LOC105371121

    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. THUMPD1 bi-allelic variants cause loss of tRNA acetylation and a syndromic neurodevelopmental disorder. Broly M, et al. Am J Hum Genet, 2022 Apr 7. PMID 35196516, Free PMC Article
    2. Pan-cancer analysis of N4-acetylcytidine adaptor THUMPD1 as a predictor for prognosis and immunotherapy. Li K, et al. Biosci Rep, 2021 Dec 22. PMID 34762107, Free PMC Article
    3. Cytosolic THUMPD1 promotes breast cancer cells invasion and metastasis via the AKT-GSK3-Snail pathway. Zhang X, et al. Oncotarget, 2017 Feb 21. PMID 28076326, Free PMC Article
    4. Yeast Kre33 and human NAT10 are conserved 18S rRNA cytosine acetyltransferases that modify tRNAs assisted by the adaptor Tan1/THUMPD1. Sharma S, et al. Nucleic Acids Res, 2015 Feb 27. PMID 25653167, Free PMC Article
    5. Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q. Loftus BJ, et al. Genomics, 1999 Sep 15. PMID 10493829

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. THUMPD1 bi-allelic variants cause loss of tRNA acetylation and a syndromic neurodevelopmental disorder.
      Title: THUMPD1 bi-allelic variants cause loss of tRNA acetylation and a syndromic neurodevelopmental disorder.
    2. Pan-cancer analysis of N4-acetylcytidine adaptor THUMPD1 as a predictor for prognosis and immunotherapy.
      Title: Pan-cancer analysis of N4-acetylcytidine adaptor THUMPD1 as a predictor for prognosis and immunotherapy.
    3. These results indicate that THUMPD1 promotes breast cancer cells invasion and migration via the AKT-GSK3beta-Snail pathway
      Title: Cytosolic THUMPD1 promotes breast cancer cells invasion and metastasis via the AKT-GSK3-Snail pathway.
    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
    Neurodevelopmental disorder with speech delay and variable ocular anomalies
    MedGen: C5774194 OMIM: 619989 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)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    nucleocapsid gag HIV-1 NC is identified to have a physical interaction with THUMP domain containing 1 (THUMPD1) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp686C1054

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in tRNA modification IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    THUMP domain-containing protein 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_001304550.2 → NP_001291479.1  THUMP domain-containing protein 1

      See identical proteins and their annotated locations for NP_001291479.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AC004381
      Consensus CDS
      CCDS10588.1
      UniProtKB/Swiss-Prot
      Q9BWC3, Q9NXG2
      UniProtKB/TrEMBL
      Q6MZT3
      Related
      ENSP00000370741.2, ENST00000381337.6
      Conserved Domains (1) summary
      cd11717
      Location:45 → 254
      THUMP_THUMPD1_like; THUMP domain-containing protein 1-like

    2. NM_017736.5 → NP_060206.2  THUMP domain-containing protein 1

      See identical proteins and their annotated locations for NP_060206.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AC004381
      Consensus CDS
      CCDS10588.1
      UniProtKB/Swiss-Prot
      Q9BWC3, Q9NXG2
      UniProtKB/TrEMBL
      Q6MZT3
      Related
      ENSP00000379392.2, ENST00000396083.7
      Conserved Domains (1) summary
      cd11717
      Location:45 → 254
      THUMP_THUMPD1_like; THUMP domain-containing protein 1-like

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      20733664..20741818 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      20664595..20672749 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NXG2.2 GenPept UniProtKB/Swiss-Prot:Q9NXG2

    Gene LinkOut

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

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