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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
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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)

Genotypes

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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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

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