EIF3CL

eukaryotic translation initiation factor 3 subunit C like, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 16:28379579-28403841

Links

ENSG00000205609 ∙ NCBI:728689 ∙ ∙ HGNC:26347 ∙ Uniprot:B5ME19 ∙ 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 EIF3CL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EIF3CL 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in EIF3CL

This is a list of pathogenic ClinVar variants found in the EIF3CL region.

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

Position	Type	Phenotype	Significance	ClinVar
16-28391803-A-C		not specified	Uncertain significance (Jan 23, 2023)
16-28391833-T-C		not specified	Uncertain significance (Aug 11, 2024)
16-28392002-C-A		not specified	Uncertain significance (Dec 31, 2024)
16-28392003-G-A		not specified	Uncertain significance (Jul 06, 2021)
16-28392009-T-C		not specified	Uncertain significance (Feb 13, 2024)
16-28392029-T-C		not specified	Uncertain significance (Jan 03, 2024)
16-28392119-T-C		not specified	Uncertain significance (Nov 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EIF3CL	protein_coding	protein_coding	ENST00000398943	20	24301

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0121	0.660	111877	1	0	111878	0.00000447

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.906	21	36.4	0.577	0.00000214	6040
Missense in Polyphen		11	15.501	0.70964		2667
Synonymous	1.23	8	13.8	0.579	8.18e-7	1704
Loss of Function	0.493	3	4.08	0.736	2.66e-7	574

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000199	0.00000993
Middle Eastern	0.00	0.00
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. 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. {ECO:0000250|UniProtKB:Q99613}.
• Pathway: RNA transport - Homo sapiens (human);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: 0.118

Haploinsufficiency Scores

• pHI: 0.255

Essentials

• essential_gene_CRISPR: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.177

Gene Damage Prediction

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

Gene ontology

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