EIF3L

eukaryotic translation initiation factor 3 subunit L, the group of Eukaryotic translation initiation factor 3

Basic information

Region (hg38): 22:37848868-37889407

Previous symbols: [ "EIF3S6IP", "EIF3EIP" ]

Links

ENSG00000100129

∙ NCBI:51386 ∙ OMIM:619197 ∙ HGNC:18138 ∙ Uniprot:Q9Y262 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EIF3L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EIF3L 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 clinvar	1
missense			10 clinvar			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	1

Variants in EIF3L

This is a list of pathogenic ClinVar variants found in the EIF3L region.

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

Position	Phenotype	Significance	ClinVar
22-37850018-G-T	not specified	Uncertain significance (Mar 07, 2024)	3087974
22-37851328-C-T	not specified	Uncertain significance (Apr 01, 2024)	3275018
22-37855565-C-T	not specified	Likely benign (Mar 15, 2024)	3275019
22-37855642-A-G	not specified	Uncertain significance (Nov 08, 2022)	2343378
22-37863301-C-T	not specified	Uncertain significance (Apr 19, 2023)	2538562
22-37875900-A-G		Benign (May 30, 2017)	777707
22-37875914-G-T	not specified	Uncertain significance (Aug 25, 2021)	2402758
22-37875992-C-G	not specified	Uncertain significance (Apr 22, 2022)	2301939
22-37875995-C-T	not specified	Uncertain significance (Sep 27, 2022)	2313797
22-37877758-C-T	not specified	Uncertain significance (Aug 02, 2023)	2615254
22-37878056-G-A	not specified	Uncertain significance (Dec 16, 2022)	2206565
22-37886795-G-A	not specified	Uncertain significance (Apr 19, 2023)	2548189
22-37888459-C-G	not specified	Uncertain significance (Sep 20, 2023)	3087973

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EIF3L	protein_coding	protein_coding	ENST00000412331	13	40540

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.838	0.162	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.70	191	329	0.581	0.0000184	3752
Missense in Polyphen		44	97.18	0.45277		1246
Synonymous	-0.0915	122	121	1.01	0.00000642	995
Loss of Function	4.30	6	32.4	0.185	0.00000146	396

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000546	0.0000544
Finnish	0.000371	0.000370
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.0000546	0.0000544
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is required for several steps in the initiation of protein synthesis (PubMed:17581632, PubMed:25849773, PubMed:27462815). The eIF-3 complex associates with the 40S ribosome and facilitates the recruitment of eIF-1, eIF-1A, eIF-2:GTP:methionyl-tRNAi and eIF-5 to form the 43S pre- initiation complex (43S PIC). The eIF-3 complex stimulates mRNA recruitment to the 43S PIC and scanning of the mRNA for AUG recognition. The eIF-3 complex is also required for disassembly and recycling of post-termination ribosomal complexes and subsequently prevents premature joining of the 40S and 60S ribosomal subunits prior to initiation (PubMed:17581632). The eIF- 3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation, including cell cycling, differentiation and apoptosis, and uses different modes of RNA stem-loop binding to exert either translational activation or repression (PubMed:25849773). {ECO:0000255|HAMAP-Rule:MF_03011, ECO:0000269|PubMed:17581632, ECO:0000269|PubMed:25849773, ECO:0000269|PubMed:27462815}.;
Pathway: Formation of the ternary complex, and subsequently, the 43S complex;Translation initiation complex formation;Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S;Eukaryotic Translation Initiation;Translation;Metabolism of proteins;Formation of a pool of free 40S subunits;Ribosomal scanning and start codon recognition;L13a-mediated translational silencing of Ceruloplasmin expression;GTP hydrolysis and joining of the 60S ribosomal subunit;Cap-dependent Translation Initiation (Consensus)

Recessive Scores

pRec: 0.123

Intolerance Scores

loftool: 0.434
rvis_EVS: -0.76
rvis_percentile_EVS: 13.33

Haploinsufficiency Scores

pHI: 0.104
hipred: Y
hipred_score: 0.775
ghis: 0.615

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: H
gene_indispensability_pred: E
gene_indispensability_score: 0.728

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Eif3l
Phenotype

Gene ontology

Biological process: formation of cytoplasmic translation initiation complex;translational initiation;viral translational termination-reinitiation
Cellular component: fibrillar center;nucleoplasm;cytosol;eukaryotic translation initiation factor 3 complex;membrane;eukaryotic 43S preinitiation complex;eukaryotic 48S preinitiation complex
Molecular function: RNA binding;translation initiation factor activity;protein binding