LAMTOR5
late endosomal/lysosomal adaptor, MAPK and MTOR activator 5, the group of Ragulator complex
Basic information
Region (hg38): 1:110401249-110407942
Previous symbols: [ "HBXIP" ]
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 LAMTOR5 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 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 7 | 0 | 0 |
Variants in LAMTOR5
This is a list of pathogenic ClinVar variants found in the LAMTOR5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-110401561-C-T | not specified | Uncertain significance (Jul 05, 2023) | ||
| 1-110403930-T-A | not specified | Uncertain significance (Dec 01, 2022) | ||
| 1-110404034-G-A | not specified | Uncertain significance (May 05, 2023) | ||
| 1-110407664-C-T | not specified | Uncertain significance (Jul 14, 2021) | ||
| 1-110407691-A-G | not specified | Uncertain significance (Oct 05, 2023) | ||
| 1-110407710-T-G | not specified | Uncertain significance (Sep 16, 2021) | ||
| 1-110407749-C-T | not specified | Uncertain significance (Oct 06, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LAMTOR5 | protein_coding | protein_coding | ENST00000256644 | 4 | 6694 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000383 | 0.218 | 125741 | 0 | 6 | 125747 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.906 | 131 | 105 | 1.25 | 0.00000516 | 1107 |
| Missense in Polyphen | 20 | 20.517 | 0.97481 | 251 | ||
| Synonymous | -0.475 | 45 | 41.1 | 1.09 | 0.00000213 | 368 |
| Loss of Function | -0.150 | 8 | 7.56 | 1.06 | 3.28e-7 | 87 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000906 | 0.0000905 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000545 | 0.0000544 |
| Finnish | 0.0000464 | 0.0000462 |
| European (Non-Finnish) | 0.00000884 | 0.00000879 |
| Middle Eastern | 0.0000545 | 0.0000544 |
| South Asian | 0.0000336 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: As part of the Ragulator complex it is involved in amino acid sensing and activation of mTORC1, a signaling complex promoting cell growth in response to growth factors, energy levels, and amino acids. Activated by amino acids through a mechanism involving the lysosomal V-ATPase, the Ragulator functions as a guanine nucleotide exchange factor activating the small GTPases Rag. Activated Ragulator and Rag GTPases function as a scaffold recruiting mTORC1 to lysosomes where it is in turn activated. When complexed to BIRC5, interferes with apoptosome assembly, preventing recruitment of pro-caspase-9 to oligomerized APAF1, thereby selectively suppressing apoptosis initiated via the mitochondrial/cytochrome c pathway. Down-regulates hepatitis B virus (HBV) replication. {ECO:0000269|PubMed:12773388, ECO:0000269|PubMed:22980980}.;
- Pathway
- mTOR signaling pathway - Homo sapiens (human);Hepatitis B - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;Signal Transduction;Gene expression (Transcription);calcium signaling by hbx of hepatitis b virus;Generic Transcription Pathway;RNA Polymerase II Transcription;mTORC1-mediated signalling;Energy dependent regulation of mTOR by LKB1-AMPK;mTOR signalling;AndrogenReceptor;TP53 Regulates Metabolic Genes;Macroautophagy;Cellular responses to external stimuli;Regulation of PTEN gene transcription;PTEN Regulation;PIP3 activates AKT signaling;Transcriptional Regulation by TP53;Intracellular signaling by second messengers
(Consensus)
Recessive Scores
- pRec
- 0.120
Intolerance Scores
- loftool
- rvis_EVS
- 0.71
- rvis_percentile_EVS
- 85.53
Haploinsufficiency Scores
- pHI
- 0.132
- hipred
- N
- hipred_score
- 0.146
- ghis
- 0.395
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- gene_indispensability_score
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lamtor5
- Phenotype
- integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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
- cell cycle arrest;regulation of cell size;response to virus;regulation of macroautophagy;viral genome replication;positive regulation of TOR signaling;negative regulation of apoptotic process;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;protein localization to lysosome;cellular response to amino acid stimulus
- Cellular component
- lysosome;lysosomal membrane;cytosol;Ragulator complex
- Molecular function
- guanyl-nucleotide exchange factor activity;protein binding;protein-containing complex scaffold activity