EFL1 (elongation factor like GTPase 1)

Gene

• Entrez ID: 79631
• Gene name: Elongation factor like GTPase 1
• Gene symbol: EFL1
• Synonyms (NCBI Gene): EFTUD1, FAM42A, HsT19294, RIA1, SDS2
• Chromosome: 15
• Chromosome location: 15q25.2

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs1316615934	A>T	Pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs1441937959	T>C	Likely-pathogenic	5 prime UTR variant, genic upstream transcript variant, missense variant, non coding transcript variant, coding sequence variant

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0003746	Function	Translation elongation factor activity	IEA
GO:0003924	Function	GTPase activity	IBA
GO:0003924	Function	GTPase activity	IDA	21536732
GO:0003924	Function	GTPase activity	IEA
GO:0005515	Function	Protein binding	IPI	30545121, 39251607
GO:0005525	Function	GTP binding	IEA
GO:0005829	Component	Cytosol	IBA
GO:0006412	Process	Translation	IEA
GO:0006414	Process	Translational elongation	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0042254	Process	Ribosome biogenesis	IEA
GO:0042256	Process	Cytosolic ribosome assembly	IBA
GO:0042256	Process	Cytosolic ribosome assembly	IEA
GO:0042256	Process	Cytosolic ribosome assembly	IMP	21536732
GO:0043022	Function	Ribosome binding	IBA
GO:0043022	Function	Ribosome binding	IMP	21536732
GO:0046039	Process	GTP metabolic process	IDA	21536732
GO:1990904	Component	Ribonucleoprotein complex	IBA

Other IDs

• MIM: 617538
• HGNC: 25789
• e!Ensembl: ENSG00000140598

Protein

• UniProt ID: Q7Z2Z2
• Protein name: Elongation factor-like GTPase 1 (EC 3.6.5.-) (Elongation factor Tu GTP-binding domain-containing protein 1) (Elongation factor-like 1) (Protein FAM42A)
• Protein function: GTPase involved in the biogenesis of the 60S ribosomal subunit and translational activation of ribosomes. Together with SBDS, triggers the GTP-dependent release of EIF6 from 60S pre-ribosomes in the cytoplasm, thereby activating ribosomes for tr
• PDB: 5ANB, 5ANC
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00009	GTP_EFTU	17 → 365	Elongation factor Tu GTP binding domain	Domain
  PF14492	EFG_III	614 → 687	Elongation Factor G, domain III	Domain
  PF00679	EFG_C	979 → 1066	Elongation factor G C-terminus	Domain

• Tissue specificity: TISSUE SPECIFICITY: Expressed at low levels in brain. Expression is highly increased in glioma tissues. {ECO:0000269|PubMed:25015090}.
• Sequence:

  MVLNSLDKMIQLQKNTANIRNICVLAHVDHGKTTLADCLISSNGIISSRLAGKLRYMDSR
  EDEQIRGITMKSSAISLHYATGNEEYLINLIDSPGHVDFSSEVSTAVRICDGCIIVVDAV
  EGVCPQTQAVLRQAWLENIRPVLVINKIDRLIVELKFTPQEAYSHLKNILEQINALTGTL
  FTSKVLEERAERETESQVNPNSEQGEQVYDWSTGLEDTDDSHLYFSPEQGNVVFTSAIDG
  WGFGIEHFARIYSQKIGIKKEVLMKTLWGDYYINMKAKKIMKGDQAKGKKPLFVQLILEN
  IWSLYDAVLKKDKDKIDKIVTSLGLKIGAREARHSDPKVQINAICSQWLPISHAVLAMVC
  QKLPSPLDITAERVERLMCTGSQTFDSFPPETQALKAAFMKCGSEDTAPVIIFVSKMFAV
  DAKALPQNKPRPLTQEEIAQRRERARQRHAEKLAAAQGQAPLEPTQDGSAIETCPKGEEP
  RGDEQQVESMTPKPVLQEENNQESFIAFARVFSGVARRGKKIFVLGPKYSPLEFLRRVPL
  GFSAPPDGLPQVPHMAYCALENLYLLMGRELEYLEEVPPGNVLGIGGLQDFVLKSATLCS
  LPSCPPFIPLNFEATPIVRVAVEPKHPSEMPQLVKGMKLLNQADPCVQILIQETGEHVLV
  TAGEVHLQRCLDDLKERFAKIHISVSEPIIPFRETITKPPKVDMVNEEIGKQQKVAVIHQ
  MKEDQSKIPEGIQVDSDGLITITTPNKLATLSVRAMPLPEEVTQILEENSDLIRSMEQLT
  SSLNEGENTHMIHQKTQEKIWEFKGKLEQHLTGRRWRNIVDQIWSFGPRKCGPNILVNKS
  EDFQNSVWTGPADKASKEASRYRDLGNSIVSGFQLATLSGPMCEEPLMGVCFVLEKWDLS
  KFEEQGASDLAKEGQEENETCSGGNENQELQDGCSEAFEKRTSQKGESPLTDCYGPFSGQ
  LIATMKEACRYALQVKPQRLMAAMYTCDIMATGDVLGRVYAVLSKREGRVLQEEMKEGTD
  MFIIKAVLPVAESFGFADEIRKRTSGLASPQLVFSHWEIIPSDPFWVPTTEEEYLHFGEK
  ADSENQARKYMNAVRKRKGLYVEEKIVEHAEKQRTLSKNK

• Sequence length: 1120

Pathways

KEGG:

Ribosome biogenesis in eukaryotes

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Shwachman syndrome	Likely pathogenic	rs1330065864, rs763132789, rs756494164, rs370108445	RCV005254037 RCV005254038 RCV005254039 RCV005254040	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Shwachman-Diamond syndrome 2	Likely pathogenic; Pathogenic	rs1330065864, rs763132789, rs2141228362, rs756494164, rs1380341628, rs370108445	RCV002248311 RCV002248312 RCV002248313 RCV002248314 RCV002248315 RCV002248316	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Adrenocortical carcinoma, hereditary	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ASTROCYTOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
EFL1-related disorder	Likely benign; Benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLIOMA	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Immunodeficiency	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SHWACHMAN-DIAMOND SYNDROME	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TOURETTE SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Anemia	Anemia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Aplastic Anemia	Aplastic anemia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Asthma	Asthma	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	25736056	Associate	★☆☆☆☆ Found in Text Mining only
Byzanthine arch palate	High palate	HPO_DG			★☆☆☆☆ Found in Text Mining only
Carotid Stenosis	Carotid artery stenosis	Pubtator	20966410	Associate	★☆☆☆☆ Found in Text Mining only
Congenital pectus carinatum	Congenital Pectus Carinatum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Insulin-Dependent	Diabetes Mellitus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Eczema	Eczema	HPO_DG			★☆☆☆☆ Found in Text Mining only
Exocrine pancreatic insufficiency	Exocrine pancreatic insufficiency	HPO_DG			★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	25015090	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ichthyoses	Ichthyosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intestinal Diseases	Intestinal disease	Pubtator	37992574	Stimulate	★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Malabsorption Syndrome	Malabsorption Syndrome	HPO_DG			★☆☆☆☆ Found in Text Mining only
Malnutrition	Malnutrition	BEFREE	28693012		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microdontia (disorder)	Microdontia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Mitochondrial Diseases	Mitochondrial disease	Pubtator	37992574	Associate	★☆☆☆☆ Found in Text Mining only
Myelodysplasia	Myelodysplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
MYELODYSPLASTIC SYNDROME	Myelodysplastic Syndrome	HPO_DG			★☆☆☆☆ Found in Text Mining only
Myopia	Myopia	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Neutropenia	Neutropenia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Normocytic anemia	Anemia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Osteopenia	Osteopenia	BEFREE	28774817		★☆☆☆☆ Found in Text Mining only
Osteopenia	Osteopenia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Pancytopenia	Pancytopenia	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Precursor T-Cell Lymphoblastic Leukemia-Lymphoma	Lymphoblastic Leukemia	BEFREE	28715419		★☆☆☆☆ Found in Text Mining only
Recurrent aphthous ulcer	Aphthous Ulcer	HPO_DG			★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Severe myopia	Myopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Shwachman syndrome	Shwachman Syndrome	BEFREE	21536732, 23831625, 24406167, 25991726, 30413969, 30545121, 30780079, 31151987, 31838967		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Shwachman syndrome	Shwachman Syndrome	ORPHANET_DG	28331068		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Shwachman-Diamond syndrome	Shwachman-Diamond Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SHWACHMAN-DIAMOND SYNDROME 2	Shwachman syndrome	UNIPROT_DG	28331068		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
SHWACHMAN-DIAMOND SYNDROME 2	Shwachman syndrome	GENOMICS_ENGLAND_DG	29970384		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
SHWACHMAN-DIAMOND SYNDROME 2	Shwachman syndrome	CLINVAR_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Sialic Acid Storage Disease, Finnish Type (disorder)	Sialic Acid Storage Disease	BEFREE	30917931		★☆☆☆☆ Found in Text Mining only
Skin Erosion	Skin Erosion	BEFREE	28774817		★☆☆☆☆ Found in Text Mining only
Specific learning disability	Specific Learning Disorder	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Strudwick syndrome	Strudwick Syndrome	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only