EIF3J

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

Basic information

Region (hg38): 15:44537124-44563029

Previous symbols: [ "EIF3S1" ]

Links

ENSG00000104131 ∙ NCBI:8669 ∙ OMIM:603910 ∙ HGNC:3270 ∙ Uniprot:O75822 ∙ 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 EIF3J gene.

• Spastic Paraplegia, Recessive (3 variants)
• Inborn genetic diseases (3 variants)
• Hereditary spastic paraplegia 11 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EIF3J 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						0
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			3			3
Total	0	0	6	0	0

Variants in EIF3J

This is a list of pathogenic ClinVar variants found in the EIF3J region.

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

Position	Type	Phenotype	Significance	ClinVar
15-44537347-G-A		not specified	Uncertain significance (Feb 22, 2023)
15-44554614-G-A		not specified	Uncertain significance (Aug 31, 2023)
15-44554620-A-G		not specified	Uncertain significance (Mar 01, 2023)
15-44557613-T-A		not specified	Uncertain significance (Feb 13, 2024)
15-44562722-A-AAAGAT		Spastic Paraplegia, Recessive	Uncertain significance (Jun 14, 2016)
15-44562733-T-G		Hereditary spastic paraplegia 11	Uncertain significance (Jan 13, 2018)
15-44562749-G-GTATC		Spastic Paraplegia, Recessive	Uncertain significance (Jun 14, 2016)
15-44562801-G-A		Spastic Paraplegia, Recessive	Uncertain significance (Jun 14, 2016)
15-44562822-C-A		Hereditary spastic paraplegia 11	Uncertain significance (Jan 13, 2018)
15-44562878-T-C		Hereditary spastic paraplegia 11 • Amyotrophic lateral sclerosis type 5 • Charcot-Marie-Tooth disease axonal type 2X	Likely benign (Oct 10, 2019)
15-44562880-G-C		Hereditary spastic paraplegia 11	Uncertain significance (Jan 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EIF3J	protein_coding	protein_coding	ENST00000261868	8	25973

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.857	0.143	125731	0	3	125734	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	91	130	0.702	0.00000616	1679
Missense in Polyphen		13	27.156	0.47872		421
Synonymous	1.55	35	48.8	0.717	0.00000246	440
Loss of Function	3.13	2	15.1	0.132	6.90e-7	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000699	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000204	0.0000176
Middle Eastern	0.0000699	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

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: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. 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:0000269|PubMed:25849773, ECO:0000269|PubMed:27462815}.
• Pathway: RNA transport - Homo sapiens (human);Translation Factors;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: 0.140

Intolerance Scores

• loftool: 0.217
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.11

Haploinsufficiency Scores

• pHI: 0.592
• hipred: Y
• hipred_score: 0.802
• ghis: 0.609

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.428

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Eif3j1

Gene ontology

• Biological process: formation of cytoplasmic translation initiation complex;translational initiation
• Cellular component: cytosol;eukaryotic translation initiation factor 3 complex;eukaryotic 43S preinitiation complex;eukaryotic 48S preinitiation complex
• Molecular function: translation initiation factor activity;protein binding