LAMTOR3

late endosomal/lysosomal adaptor, MAPK and MTOR activator 3, the group of Ragulator complex

Basic information

Region (hg38): 4:99878336-99894428

Previous symbols: [ "MAP2K1IP1", "MAPKSP1" ]

Links

ENSG00000109270 ∙ NCBI:8649 ∙ OMIM:603296 ∙ HGNC:15606 ∙ Uniprot:Q9UHA4 ∙ 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 LAMTOR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LAMTOR3 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in LAMTOR3

This is a list of pathogenic ClinVar variants found in the LAMTOR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-99882008-C-A		not specified	Uncertain significance (Jan 16, 2024)
4-99882056-T-C		not specified	Uncertain significance (Mar 29, 2022)
4-99884076-C-T		not specified	Uncertain significance (Jan 19, 2024)
4-99884116-A-G		not specified	Uncertain significance (May 26, 2022)
4-99885559-A-T		not specified	Uncertain significance (May 14, 2024)
4-99885650-A-C		not specified	Uncertain significance (Jun 06, 2023)
4-99887308-G-C		not specified	Uncertain significance (May 16, 2023)
4-99887337-G-C		not specified	Uncertain significance (Feb 16, 2023)
4-99892015-T-C		not specified	Uncertain significance (Jan 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LAMTOR3	protein_coding	protein_coding	ENST00000499666	6	16155

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.731	0.266	125274	0	2	125276	0.00000798

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0444	58	59.0	0.984	0.00000273	796
Missense in Polyphen		12	13.795	0.8699		185
Synonymous	1.62	11	20.3	0.543	8.74e-7	232
Loss of Function	2.41	1	8.66	0.115	5.29e-7	101

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	0.0000463	0.0000462
European (Non-Finnish)	0.00000893	0.00000881
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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. Adapter protein that enhances the efficiency of the MAP kinase cascade facilitating the activation of MAPK2. {ECO:0000269|PubMed:20381137, ECO:0000269|PubMed:22980980}.
• Pathway: mTOR signaling pathway - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);EGF-Ncore;miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;MAPK Signaling Pathway;MAP2K and MAPK activation;Neutrophil degranulation;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;mTORC1-mediated signalling;Energy dependent regulation of mTOR by LKB1-AMPK;mTOR signalling;Innate Immune System;Immune System;TP53 Regulates Metabolic Genes;Macroautophagy;Cellular responses to external stimuli;Regulation of PTEN gene transcription;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;PTEN Regulation;PIP3 activates AKT signaling;Transcriptional Regulation by TP53;Intracellular signaling by second messengers (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• pHI: 0.354
• hipred: Y
• hipred_score: 0.671
• ghis: 0.670

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Lamtor3

Gene ontology

• Biological process: MAPK cascade;activation of MAPKK activity;cell cycle arrest;regulation of macroautophagy;positive regulation of TOR signaling;cellular protein localization;neutrophil degranulation;cellular response to amino acid stimulus
• Cellular component: lysosomal membrane;plasma membrane;focal adhesion;endosome membrane;specific granule membrane;extracellular exosome;tertiary granule membrane;Ragulator complex
• Molecular function: guanyl-nucleotide exchange factor activity;protein binding;kinase activator activity;protein-containing complex scaffold activity