LAMTOR4

late endosomal/lysosomal adaptor, MAPK and MTOR activator 4, the group of Ragulator complex

Basic information

Region (hg38): 7:100148912-100155944

Previous symbols: [ "C7orf59" ]

Links

ENSG00000188186 ∙ NCBI:389541 ∙ OMIM:618834 ∙ HGNC:33772 ∙ Uniprot:Q0VGL1 ∙ 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 LAMTOR4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LAMTOR4 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					2	2
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	2

Variants in LAMTOR4

This is a list of pathogenic ClinVar variants found in the LAMTOR4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-100149565-G-A		not specified	Uncertain significance (Jul 26, 2022)
7-100149574-C-G		not specified	Uncertain significance (Feb 13, 2023)
7-100153403-T-A		not specified	Uncertain significance (Oct 25, 2023)
7-100153475-C-T		not specified	Uncertain significance (Sep 30, 2022)
7-100153476-G-A		not specified	Uncertain significance (Sep 27, 2022)
7-100153481-C-T		not specified	Uncertain significance (Oct 29, 2024)
7-100153491-T-C		not specified	Uncertain significance (Sep 16, 2021)
7-100153882-A-G		not specified	Uncertain significance (Mar 24, 2023)
7-100153893-G-A		not specified	Uncertain significance (Jun 17, 2024)
7-100153898-G-A			Benign (Aug 01, 2024)
7-100153961-C-G			Benign (May 25, 2018)
7-100155046-C-T		not specified	Uncertain significance (Jan 24, 2024)
7-100155084-T-G		Microcephaly 25, primary, autosomal recessive	Uncertain significance (Sep 30, 2019)
7-100155414-G-A			Likely benign (Aug 01, 2023)
7-100155498-A-G		Microcephaly 25, primary, autosomal recessive	Benign (Jul 14, 2021)
7-100155801-C-T		TRAPPC14-related disorder	Likely benign (May 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LAMTOR4	protein_coding	protein_coding	ENST00000341942	4	7038

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00356	0.641	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.268	49	54.6	0.898	0.00000306	606
Missense in Polyphen		8	12.506	0.63971		160
Synonymous	-0.544	27	23.6	1.14	0.00000121	216
Loss of Function	0.524	4	5.30	0.755	2.26e-7	56

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000906	0.0000906
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000529	0.0000527
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. {ECO:0000269|PubMed:22980980}.
• Pathway: mTOR signaling pathway - Homo sapiens (human);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;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: 0.107

Intolerance Scores

• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.231
• ghis: 0.591

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lamtor4

Gene ontology

• Biological process: cell cycle arrest;regulation of cell size;regulation of macroautophagy;positive regulation of TOR signaling;protein localization to lysosome;cellular response to amino acid stimulus
• Cellular component: lysosome;lysosomal membrane;intracellular membrane-bounded organelle;Ragulator complex
• Molecular function: guanyl-nucleotide exchange factor activity;protein binding;protein-containing complex scaffold activity