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

Gene ID: 55623, updated on 3-Nov-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, Nov 2024]
Expression
Ubiquitous expression in prostate (RPKM 15.3), endometrium (RPKM 11.9) and 25 other tissues See more
Orthologs
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (20733664..20741818, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (20664595..20672749, complement)
RS_2024_09 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 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. 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
  2. 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
  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 (39) 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_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
    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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