EFL1

elongation factor like GTPase 1, the group of Ribosomal biogenesis factors

Basic information

Region (hg38): 15:82130206-82262773

Previous symbols: [ "EFTUD1" ]

Links

ENSG00000140598 ∙ NCBI:79631 ∙ OMIM:617538 ∙ HGNC:25789 ∙ Uniprot:Q7Z2Z2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Shwachman-Diamond syndrome 2 (Moderate), mode of inheritance: AR
• Shwachman-Diamond syndrome (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Shwachman-Diamond syndrome 2	AR	Allergy/Immunology/Infectious; Gastrointestinal; Hematologic	Medical treatment (eg, pancreatic enzymes, fat-soluble vitamins) can be effective to treat pancreatic exocrine insufficiency; Blood/platelet transfusions may be necessary; Due to neutropenia and infectious risk, prophylactic measures (eg antibiotics), as well as early and aggressive treatment of infections, may be beneficial	Allergy/Immunology/Infectious; Craniofacial; Gastrointestinal; Hematologic; Musculoskeletal; Neurologic	28331068

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EFL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EFL1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	113	3	117
missense		1	201	4	13	219
nonsense			6			6
start loss			1			1
frameshift			2			2
inframe indel			1			1
splice donor/acceptor (+/-2bp)			2			2
splice region			8	11	1	20
non coding			2	52	6	60
Total	0	1	216	169	22

Variants in EFL1

This is a list of pathogenic ClinVar variants found in the EFL1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-82130388-G-A			Likely benign (Mar 22, 2023)
15-82130404-T-C			Uncertain significance (Nov 14, 2021)
15-82130448-C-T			Likely benign (Oct 17, 2023)
15-82130452-C-T		Shwachman-Diamond syndrome 2	Conflicting classifications of pathogenicity (Nov 14, 2023)
15-82130453-G-A			Uncertain significance (Jul 21, 2022)
15-82130459-C-T			Uncertain significance (Feb 02, 2023)
15-82130460-G-A			Likely benign (Jan 17, 2024)
15-82130465-T-G		Shwachman-Diamond syndrome 2	Uncertain significance (Feb 23, 2023)
15-82130469-C-T			Likely benign (Apr 17, 2023)
15-82130472-C-A			Likely benign (May 16, 2022)
15-82130475-G-A			Likely benign (Sep 19, 2023)
15-82130502-C-T			Likely benign (Jul 16, 2023)
15-82130503-C-T		Inborn genetic diseases	Uncertain significance (Nov 17, 2021)
15-82130517-T-C			Likely benign (Nov 22, 2023)
15-82130528-T-A			Uncertain significance (Sep 24, 2021)
15-82130531-T-C		Shwachman-Diamond syndrome 2	Pathogenic (Apr 18, 2022)
15-82130533-G-A			Uncertain significance (Feb 20, 2022)
15-82130544-G-A			Likely benign (Jul 02, 2021)
15-82130568-AAAG-A			Uncertain significance (Sep 19, 2021)
15-82130577-G-A			Likely benign (Nov 18, 2023)
15-82138638-A-T			Likely benign (Dec 30, 2023)
15-82138642-G-C			Likely benign (Apr 29, 2022)
15-82138666-G-A			Uncertain significance (Aug 06, 2022)
15-82138668-C-T			Uncertain significance (Aug 19, 2022)
15-82138679-T-A			Uncertain significance (Aug 24, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EFL1	protein_coding	protein_coding	ENST00000268206	19	132534

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.12e-8	1.00	124719	0	77	124796	0.000309

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	507	593	0.855	0.0000296	7376
Missense in Polyphen		135	197.28	0.68431		2302
Synonymous	0.260	197	202	0.977	0.00000995	2114
Loss of Function	4.27	23	58.1	0.396	0.00000330	662

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000720	0.000655
Ashkenazi Jewish	0.000696	0.000695
East Asian	0.000170	0.000167
Finnish	0.000373	0.000371
European (Non-Finnish)	0.000348	0.000344
Middle Eastern	0.000170	0.000167
South Asian	0.000169	0.000163
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: 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 translation competence by allowing 80S ribosome assembly and facilitating EIF6 recycling to the nucleus, where it is required for 60S rRNA processing and nuclear export. Has low intrinsic GTPase activity. GTPase activity is increased by contact with 60S ribosome subunits. {ECO:0000269|PubMed:21536732}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• rvis_EVS: 0.83
• rvis_percentile_EVS: 88.09

Haploinsufficiency Scores

• pHI: 0.297
• hipred: N
• hipred_score: 0.476
• ghis: 0.479

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Efl1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: translational elongation;mature ribosome assembly;GTP metabolic process
• Cellular component: cytosol;ribonucleoprotein complex
• Molecular function: translation elongation factor activity;GTPase activity;GTP binding;ribosome binding