EIF3M
eukaryotic translation initiation factor 3 subunit M, the group of Armadillo like helical domain containing|Eukaryotic translation initiation factor 3
Basic information
Region (hg38): 11:32583798-32606264
Previous symbols: [ "PCID1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the EIF3M 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 3 | |||||
| Total | 0 | 0 | 10 | 0 | 0 |
Variants in EIF3M
This is a list of pathogenic ClinVar variants found in the EIF3M region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 11-32588675-T-C | not specified | Uncertain significance (Feb 08, 2023) | ||
| 11-32588698-C-T | not specified | Uncertain significance (May 02, 2024) | ||
| 11-32588710-C-T | not specified | Uncertain significance (May 24, 2023) | ||
| 11-32589605-G-T | not specified | Uncertain significance (Feb 05, 2024) | ||
| 11-32594979-C-T | not specified | Uncertain significance (Nov 19, 2024) | ||
| 11-32596038-G-C | not specified | Uncertain significance (Mar 19, 2024) | ||
| 11-32600695-T-C | not specified | Uncertain significance (Jan 06, 2023) | ||
| 11-32600763-A-G | not specified | Uncertain significance (Jan 09, 2024) | ||
| 11-32602290-A-G | not specified | Uncertain significance (Mar 18, 2024) | ||
| 11-32602345-G-C | not specified | Uncertain significance (Jun 28, 2022) | ||
| 11-32602354-T-A | not specified | Uncertain significance (Sep 22, 2022) | ||
| 11-32602831-T-G | not specified | Uncertain significance (Nov 11, 2024) | ||
| 11-32602839-G-C | not specified | Uncertain significance (Dec 18, 2023) | ||
| 11-32602840-T-C | not specified | Uncertain significance (May 10, 2024) | ||
| 11-32602871-G-T | not specified | Uncertain significance (Mar 25, 2024) | ||
| 11-32602925-G-C | not specified | Uncertain significance (Apr 25, 2023) | ||
| 11-32602995-G-A | not specified | Uncertain significance (Feb 07, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| EIF3M | protein_coding | protein_coding | ENST00000531120 | 11 | 22465 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0175 | 0.982 | 125737 | 0 | 11 | 125748 | 0.0000437 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.966 | 156 | 194 | 0.805 | 0.00000962 | 2479 |
| Missense in Polyphen | 31 | 44.254 | 0.7005 | 636 | ||
| Synonymous | 1.16 | 56 | 68.2 | 0.821 | 0.00000345 | 669 |
| Loss of Function | 2.92 | 7 | 21.6 | 0.323 | 0.00000107 | 272 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000181 | 0.000181 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000353 | 0.0000352 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000658 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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:17403899, 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:17403899). 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_03012, ECO:0000269|PubMed:17403899, 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;TCR;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
- 0.120
Intolerance Scores
- loftool
- 0.390
- rvis_EVS
- -0.18
- rvis_percentile_EVS
- 39.95
Haploinsufficiency Scores
- pHI
- 0.541
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.675
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.910
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Eif3m
- Phenotype
- growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); renal/urinary system phenotype; embryo phenotype; liver/biliary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- formation of cytoplasmic translation initiation complex;cytoplasmic translational initiation;translational initiation
- Cellular component
- cytosol;eukaryotic translation initiation factor 3 complex;eukaryotic 43S preinitiation complex;eukaryotic 48S preinitiation complex;eukaryotic translation initiation factor 3 complex, eIF3m
- Molecular function
- translation initiation factor activity;protein binding;translation initiation factor binding