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EFL1 elongation factor like GTPase 1 [ Homo sapiens (human) ]

Gene ID: 79631, updated on 27-Nov-2024

Summary

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Official Symbol
EFL1provided by HGNC
Official Full Name
elongation factor like GTPase 1provided by HGNC
Primary source
HGNC:HGNC:25789
See related
Ensembl:ENSG00000140598 MIM:617538; AllianceGenome:HGNC:25789
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
RIA1; SDS2; EFTUD1; FAM42A; HsT19294
Summary
Enables GTPase activity and ribosome binding activity. Involved in GTP metabolic process and cytosolic ribosome assembly. Predicted to be part of ribonucleoprotein complex. Predicted to be active in cytosol. Implicated in Shwachman-Diamond syndrome. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in testis (RPKM 7.4), small intestine (RPKM 6.4) and 25 other tissues See more
Orthologs
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Genomic context

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See EFL1 in Genome Data Viewer
Location:
15q25.2
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (82130233..82262734, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (79994284..80126851, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (82422574..82555075, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6744 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:82338662-82339608 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:82350032-82350532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:82350533-82351033 Neighboring gene mex-3 RNA binding family member B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6746 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:82375549-82375651 Neighboring gene uncharacterized LOC105370924 Neighboring gene long intergenic non-protein coding RNA 1583 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr15:82392793-82393305 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6747 Neighboring gene RNA, U1 small nuclear 77, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9960 Neighboring gene MPRA-validated peak2402 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr15:82553005-82553191 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9961 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9962 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:82559427-82559987 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9963 Neighboring gene stabilizer of axonemal microtubules 2 Neighboring gene ADAMTS7 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:82611132-82611632 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:82611633-82612133 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:82621782-82622282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:82622283-82622783

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. Functional analysis of a novel glioma antigen, EFTUD1. Saito K, et al. Neuro Oncol, 2014 Dec. PMID 25015090, Free PMC Article
  2. Mutations in EFL1, an SBDS partner, are associated with infantile pancytopenia, exocrine pancreatic insufficiency and skeletal anomalies in aShwachman-Diamond like syndrome. Stepensky P, et al. J Med Genet, 2017 Aug. PMID 28331068
  3. Exploring the role of elongation Factor-Like 1 (EFL1) in Shwachman-Diamond syndrome through molecular dynamics. Delre P, et al. J Biomol Struct Dyn, 2020 Oct. PMID 31838967
  4. Defective Guanine Nucleotide Exchange in the Elongation Factor-like 1 (EFL1) GTPase by Mutations in the Shwachman-Diamond Syndrome Protein. García-Márquez A, et al. J Biol Chem, 2015 Jul 17. PMID 25991726, Free PMC Article
  5. EFL1 mutations impair eIF6 release to cause Shwachman-Diamond syndrome. Tan S, et al. Blood, 2019 Jul 18. PMID 31151987, Free PMC Article

See all (42) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Somatic uniparental disomy mitigates the most damaging EFL1 allele combination in Shwachman-Diamond syndrome.
    Title: Somatic uniparental disomy mitigates the most damaging EFL1 allele combination in Shwachman-Diamond syndrome.
  2. Exploring the role of elongation Factor-Like 1 (EFL1) in Shwachman-Diamond syndrome through molecular dynamics.
    Title: Exploring the role of elongation Factor-Like 1 (EFL1) in Shwachman-Diamond syndrome through molecular dynamics.
  3. Whole exome sequencing discloses heterozygous variants in the DNAJC21 and EFL1 genes but not in SRP54 in 6 out of 16 patients with Shwachman-Diamond Syndrome carrying biallelic SBDS mutations.
    Title: Whole exome sequencing discloses heterozygous variants in the DNAJC21 and EFL1 genes but not in SRP54 in 6 out of 16 patients with Shwachman-Diamond Syndrome carrying biallelic SBDS mutations.
  4. we report biallelic mutations in EFL1 in 3 unrelated individuals with clinical features of SDS. Cellular defects in these individuals include impaired ribosomal subunit joining and attenuated global protein translation as a consequence of defective eIF6 eviction.
    Title: EFL1 mutations impair eIF6 release to cause Shwachman-Diamond syndrome.
  5. the effect of SBDS mutations on the interaction with EFL1were tested, and showed that all tested mutations disrupted the binding to EFL1.
    Title: Interaction of the GTPase Elongation Factor Like-1 with the Shwachman-Diamond Syndrome Protein and Its Missense Mutations.
  6. Mutations in EFL1 clinically manifest phenotypes of infantile pancytopenia, exocrine pancreatic insufficiency and skeletal anomalies. Mutant EFL1 proteins do not promote the release of yeast cytoplasmic Tif6 from the 60S subunit, likely preventing the formation of mature ribosomes.
    Title: Mutations in EFL1, an SBDS partner, are associated with infantile pancytopenia, exocrine pancreatic insufficiency and skeletal anomalies in aShwachman-Diamond like syndrome.
  7. Association of Elongation Factor-like 1 (EFL1) GTPase to SBDS did not modify the affinity for GTP but dramatically decreased that for GDP by increasing the dissociation rate of the nucleotide.
    Title: Defective Guanine Nucleotide Exchange in the Elongation Factor-like 1 (EFL1) GTPase by Mutations in the Shwachman-Diamond Syndrome Protein.
  8. Upon EFL1 binding, SBDS is repositioned around helix 69, thus facilitating a conformational switch in EFL1 that displaces eIF6 by competing for an overlapping binding site on the 60S ribosomal subunit.
    Title: Mechanism of eIF6 release from the nascent 60S ribosomal subunit.
  9. Downregulation of EFTUD1 induced cell-cycle arrest and apoptosis in gliomas by impairing ribosome biogenesis
    Title: Functional analysis of a novel glioma antigen, EFTUD1.
  10. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genomewide linkage and peakwide association analyses of carotid plaque in Caribbean Hispanics.
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
Shwachman-Diamond syndrome 2
MedGen: C4693704 OMIM: 617941 GeneReviews: Shwachman-Diamond Syndrome
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat downregulates the expression of elongation factor Tu GTP binding domain containing 1 (EFTUD1) in human primary T cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ13119

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 GTPase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ribosome binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ribosome binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables translation elongation factor activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in GTP metabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cytosolic ribosome assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in cytosolic ribosome assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in translational elongation IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of ribonucleoprotein complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
elongation factor-like GTPase 1
Names
elongation factor Tu GTP binding domain containing 1
elongation factor Tu GTP-binding domain-containing protein 1
elongation factor-like 1
ribosome assembly 1 homolog

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_001040610.3 → NP_001035700.1  elongation factor-like GTPase 1 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks two in-frame exons in the 5' coding region, compared to variant 1, which results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AC026624, AC026956, BC014628
    Consensus CDS
    CCDS42070.1
    UniProtKB/TrEMBL
    H0YKI9
    Related
    ENSP00000352418.3, ENST00000359445.8
    Conserved Domains (6) summary
    cd01681
    Location:636 → 935
    aeEF2_snRNP_like_IV; This family represents domain IV of archaeal and eukaryotic elongation factor 2 (aeEF-2) and of an evolutionarily conserved U5 snRNP-specific protein. U5 snRNP is a GTP-binding factor closely related to the ribosomal translocase EF-2. In complex with GTP, ...
    cd04096
    Location:932 → 1010
    eEF2_snRNP_like_C; eEF2_snRNP_like_C: this family represents a C-terminal domain of eukaryotic elongation factor 2 (eEF-2) and a homologous domain of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart ...
    PTZ00416
    Location:1 → 1052
    PTZ00416; elongation factor 2; Provisional
    cd16268
    Location:451 → 549
    EF2_II; Domain II of Elongation Factor 2
    cd16261
    Location:565 → 636
    EF2_snRNP_III; Domain III of Elongation Factor 2 (EF2)
    cl21455
    Location:20 → 202
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  2. NM_001322844.2 → NP_001309773.1  elongation factor-like GTPase 1 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC026624, AC026956
    UniProtKB/TrEMBL
    B3KPR5
    Conserved Domains (4) summary
    cd01681
    Location:424 → 723
    aeEF2_snRNP_like_IV; This family represents domain IV of archaeal and eukaryotic elongation factor 2 (aeEF-2) and of an evolutionarily conserved U5 snRNP-specific protein. U5 snRNP is a GTP-binding factor closely related to the ribosomal translocase EF-2. In complex with GTP, ...
    cd04096
    Location:720 → 798
    eEF2_snRNP_like_C; eEF2_snRNP_like_C: this family represents a C-terminal domain of eukaryotic elongation factor 2 (eEF-2) and a homologous domain of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart ...
    cd16268
    Location:239 → 337
    EF2_II; Domain II of Elongation Factor 2
    cd16261
    Location:353 → 424
    EF2_snRNP_III; Domain III of Elongation Factor 2 (EF2)

  3. NM_001322845.2 → NP_001309774.1  elongation factor-like GTPase 1 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC026624, AC026956
    Consensus CDS
    CCDS42071.1
    UniProtKB/Swiss-Prot
    A6NKY5, B7Z6I0, Q7Z2Z2, Q9H8Z6
    UniProtKB/TrEMBL
    H0YKI9
    Related
    ENSP00000512564.1, ENST00000696330.1
    Conserved Domains (1) summary
    cl30786
    Location:1 → 1103
    FusA; Translation elongation factor EF-G, a GTPase [Translation, ribosomal structure and biogenesis]

  4. NM_024580.6 → NP_078856.4  elongation factor-like GTPase 1 isoform 1

    See identical proteins and their annotated locations for NP_078856.4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the the longest isoform (1).
    Source sequence(s)
    AC026624, AC026956, BC014628
    Consensus CDS
    CCDS42071.1
    UniProtKB/Swiss-Prot
    A6NKY5, B7Z6I0, Q7Z2Z2, Q9H8Z6
    UniProtKB/TrEMBL
    H0YKI9
    Related
    ENSP00000268206.7, ENST00000268206.12
    Conserved Domains (1) summary
    cl30786
    Location:1 → 1103
    FusA; Translation elongation factor EF-G, a GTPase [Translation, ribosomal structure and biogenesis]

RNA

  1. NR_136410.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC026624, AC026956
    Related
    ENST00000696336.1

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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    82130233..82262734 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024450048.2 → XP_024305816.1  elongation factor-like GTPase 1 isoform X1

    UniProtKB/TrEMBL
    A0A8Q3SIM9
    Related
    ENSP00000512563.1, ENST00000696327.1
    Conserved Domains (1) summary
    cl27769
    Location:29 → 567
    GTP_EFTU; Elongation factor Tu GTP binding domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    79994284..80126851 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054378772.1 → XP_054234747.1  elongation factor-like GTPase 1 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7Z2Z2.2 GenPept UniProtKB/Swiss-Prot:Q7Z2Z2

Gene LinkOut

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