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

Summary

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: mouse all
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Genomic context

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_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
Downregulation of EFTUD1 induced cell-cycle arrest and apoptosis in gliomas by impairing ribosome biogenesis
Title: Functional analysis of a novel glioma antigen, EFTUD1.
Observational study of gene-disease association. (HuGE Navigator)
Title: Genomewide linkage and peakwide association analyses of carotid plaque in Caribbean Hispanics.

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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	Compare labs

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

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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

SGC30254 (e-PCR)
- UniSTS:19780

G54067 (e-PCR)
- UniSTS:109449

RH45867 (e-PCR)
- UniSTS:82314

SHGC-144354 (e-PCR)
- UniSTS:172209

A007G38 (e-PCR)
- UniSTS:16322

1990 (e-PCR)
- UniSTS:69585

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)

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
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)
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]
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

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

NC_000015.10 Reference GRCh38.p14 Primary Assembly

Range

82130233..82262734 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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