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    EFTUD2 elongation factor Tu GTP binding domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 9343, updated on 3-Nov-2024

    Summary

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    Official Symbol
    EFTUD2provided by HGNC
    Official Full Name
    elongation factor Tu GTP binding domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:30858
    See related
    Ensembl:ENSG00000108883 MIM:603892; AllianceGenome:HGNC:30858
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    MFDM; MFDGA; Snu114; Snrp116; SNRNP116; U5-116KD
    Summary
    This gene encodes a GTPase which is a component of the spliceosome complex which processes precursor mRNAs to produce mature mRNAs. Mutations in this gene are associated with mandibulofacial dysostosis with microcephaly. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]
    Expression
    Ubiquitous expression in testis (RPKM 15.7), appendix (RPKM 15.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See EFTUD2 in Genome Data Viewer
    Location:
    17q21.31
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (44849948..44899445, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (45703842..45753329, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (42927316..42976813, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:42835997-42836548 Neighboring gene ADAM metallopeptidase domain 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42853416-42853916 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:42856011-42856852 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8601 Neighboring gene gap junction protein gamma 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8602 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:42907313-42908286 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:42908287-42909260 Neighboring gene HIG1 hypoxia inducible domain family member 1B Neighboring gene ReSE screen-validated silencer GRCh37_chr17:42943931-42944112 Neighboring gene RNA, 7SL, cytoplasmic 405, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:42969539-42970081 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12266 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8603 Neighboring gene dynein axonemal assembly factor 19 Neighboring gene family with sequence similarity 187 member A Neighboring gene uncharacterized LOC105371793 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42997401-42997900 Neighboring gene glial fibrillary acidic protein Neighboring gene kinesin family member 18B

    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. Mandibulofacial dysostosis with microcephaly: An expansion of the phenotype via parental survey. Abell K, et al. Am J Med Genet A, 2021 Feb. PMID 33247512, Free PMC Article
    2. A novel EFTUD2 mutation identified an adult male with mandibulofacial dysostosis Guion-Almeida type. Narumi-Kishimoto Y, et al. Clin Dysmorphol, 2020 Oct. PMID 32541334
    3. Architecture of the spliceosome. van der Feltz C, et al. Biochemistry, 2012 Apr 24. PMID 22471593
    4. "Mandibulofacial dysostosis with microcephaly" caused by EFTUD2 mutations: expanding the phenotype. Luquetti DV, et al. Am J Med Genet A, 2013 Jan. PMID 23239648, Free PMC Article
    5. Oto-facial syndrome and esophageal atresia, intellectual disability and zygomatic anomalies - expanding the phenotypes associated with EFTUD2 mutations. Voigt C, et al. Orphanet J Rare Dis, 2013 Jul 24. PMID 23879989, Free PMC Article

    See all (268) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification of novel mutations in EYA3 and EFTUD2 in a family with craniofacial microsomia: evidence of digenic inheritance.
      Title: Identification of novel mutations in EYA3 and EFTUD2 in a family with craniofacial microsomia: evidence of digenic inheritance.
    2. The Spliceosome Factor EFTUD2 Promotes IFN Anti-HBV Effect through mRNA Splicing.
      Title: The Spliceosome Factor EFTUD2 Promotes IFN Anti-HBV Effect through mRNA Splicing.
    3. The Pregnancy Zone Protein (PZP) is significantly downregulated in the placenta of preeclampsia and HELLP syndrome patients.
      Title: The Pregnancy Zone Protein (PZP) is significantly downregulated in the placenta of preeclampsia and HELLP syndrome patients.
    4. Association of Elongation Factor Tu GTP-binding Domain-containing 2 Gene (EFTUD2) Polymorphism with the Risk of Hepatitis B Virus Infection.
      Title: Association of Elongation Factor Tu GTP-binding Domain-containing 2 Gene (EFTUD2) Polymorphism with the Risk of Hepatitis B Virus Infection.
    5. EFTUD2 missense variants disrupt protein function and splicing in mandibulofacial dysostosis Guion-Almeida type.
      Title: EFTUD2 missense variants disrupt protein function and splicing in mandibulofacial dysostosis Guion-Almeida type.
    6. Spliceosome protein EFTUD2 is upregulated in the trophoblast of spontaneous miscarriage and hydatidiform mole.
      Title: Spliceosome protein EFTUD2 is upregulated in the trophoblast of spontaneous miscarriage and hydatidiform mole.
    7. Mandibulofacial dysostosis with microcephaly: An expansion of the phenotype via parental survey.
      Title: Mandibulofacial dysostosis with microcephaly: An expansion of the phenotype via parental survey.
    8. A novel EFTUD2 mutation identified an adult male with mandibulofacial dysostosis Guion-Almeida type.
      Title: A novel EFTUD2 mutation identified an adult male with mandibulofacial dysostosis Guion-Almeida type.
    9. EFTUD2 maintains the survival of tumor cells and promotes hepatocellular carcinoma progression via the activation of STAT3.
      Title: EFTUD2 maintains the survival of tumor cells and promotes hepatocellular carcinoma progression via the activation of STAT3.
    10. report 2 cases of mandibulofacial dysostosis with microcephaly (MFDM) with different and novel de novo mutations in the elongation factor Tu GTP binding domain containing 2 gene
      Title: Novel De Novo EFTUD2 Mutations in 2 Cases With MFDM, Initially Suspected to Have Alternative Craniofacial Diagnoses.
    Submit: New GeneRIF Correction See all GeneRIFs (24)

    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

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2013-05-23)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2013-05-23)

    ClinGen Genome Curation PagePubMed

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    • FLJ44695, KIAA0031, DKFZp686E24196

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables GTPase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA binding HDA PubMed 
    enables U5 snRNA 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 cellular response to xenobiotic stimulus IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA splicing, via spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in response to cocaine IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Cajal body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of U2-type catalytic step 2 spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U2-type catalytic step 2 spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of U2-type precatalytic spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of U4/U6 x U5 tri-snRNP complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U4/U6 x U5 tri-snRNP complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of U4/U6 x U5 tri-snRNP complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of catalytic step 2 spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in membrane HDA PubMed 
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    116 kDa U5 small nuclear ribonucleoprotein component
    Names
    SNU114 homolog
    U5 snRNP-specific protein, 116 kDa
    elongation factor Tu GTP-binding domain-containing protein 2
    hSNU114

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_032674.1 RefSeqGene

      Range
      5181..54678
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001142605.2 → NP_001136077.1  116 kDa U5 small nuclear ribonucleoprotein component isoform b

      See identical proteins and their annotated locations for NP_001136077.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and in the 5' coding region, compared to variant 1. These differences causes translation initiation at a downstream AUG and results an isoform (b) with a shorter N-terminus compared to isoform a.
      Source sequence(s)
      AC015936, AK126464, BC002360, DC353274
      Consensus CDS
      CCDS45707.1
      UniProtKB/TrEMBL
      A8KAP3, Q6IBM8
      Related
      ENSP00000385873.2, ENST00000402521.7
      Conserved Domains (2) summary
      pfam16004
      Location:19 → 75
      EFTUD2; 116 kDa U5 small nuclear ribonucleoprotein component N-terminus
      cl27769
      Location:87 → 919
      GTP_EFTU; Elongation factor Tu GTP binding domain

    2. NM_001258353.2 → NP_001245282.1  116 kDa U5 small nuclear ribonucleoprotein component isoform a

      See identical proteins and their annotated locations for NP_001245282.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Both variants 1 and 3 encode the same protein.
      Source sequence(s)
      AC015936, AK128148
      Consensus CDS
      CCDS11489.1
      UniProtKB/Swiss-Prot
      B4DK30, B4DMC0, D3DX58, K7EJ81, Q15029, Q9BUR0
      UniProtKB/TrEMBL
      A8KAP3, Q6IBM8
      Related
      ENSP00000467805.1, ENST00000591382.5
      Conserved Domains (2) summary
      cl30786
      Location:122 → 954
      FusA; Translation elongation factor EF-G, a GTPase [Translation, ribosomal structure and biogenesis]
      pfam16004
      Location:4 → 110
      EFTUD2; 116 kDa U5 small nuclear ribonucleoprotein component N-terminus

    3. NM_001258354.2 → NP_001245283.1  116 kDa U5 small nuclear ribonucleoprotein component isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 5' coding region compared to variant 1. The resulting protein (isoform c) is shorter compared to isoform a.
      Source sequence(s)
      AC015936, AK297392
      Consensus CDS
      CCDS59295.1
      UniProtKB/TrEMBL
      A8KAP3, Q6IBM8
      Related
      ENSP00000465058.1, ENST00000592576.5
      Conserved Domains (2) summary
      pfam16004
      Location:4 → 110
      EFTUD2; 116 kDa U5 small nuclear ribonucleoprotein component N-terminus
      cl27769
      Location:122 → 944
      GTP_EFTU; Elongation factor Tu GTP binding domain

    4. NM_004247.4 → NP_004238.3  116 kDa U5 small nuclear ribonucleoprotein component isoform a

      See identical proteins and their annotated locations for NP_004238.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a). Both variants 1 and 3 encode the same protein.
      Source sequence(s)
      AC015936, AK126464, BC002360, DC353274
      Consensus CDS
      CCDS11489.1
      UniProtKB/Swiss-Prot
      B4DK30, B4DMC0, D3DX58, K7EJ81, Q15029, Q9BUR0
      UniProtKB/TrEMBL
      A8KAP3, Q6IBM8
      Related
      ENSP00000392094.1, ENST00000426333.7
      Conserved Domains (2) summary
      cl30786
      Location:122 → 954
      FusA; Translation elongation factor EF-G, a GTPase [Translation, ribosomal structure and biogenesis]
      pfam16004
      Location:4 → 110
      EFTUD2; 116 kDa U5 small nuclear ribonucleoprotein component N-terminus

    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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      44849948..44899445 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047437084.1 → XP_047293040.1  116 kDa U5 small nuclear ribonucleoprotein component isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      45703842..45753329 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054317819.1 → XP_054173794.1  116 kDa U5 small nuclear ribonucleoprotein component isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q15029.1 GenPept UniProtKB/Swiss-Prot:Q15029

    Gene LinkOut

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

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