LAMTOR2

Summary

LAMTOR2 (late endosomal/lysosomal adaptor, MAPK and MTOR activator 2, HGNC:29796) is a protein-coding gene on chromosome 1q22, encoding Ragulator complex protein LAMTOR2 (Q9Y2Q5). 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. It is a selective cancer dependency (DepMap: 61.7% of cell lines).

The product of this gene is highly conserved with a mouse protein associated with the cytoplasmic face of late endosomes and lysosomes. The mouse protein interacts with MAPK scaffold protein 1, a component of the mitogen-activated protein kinase pathway. In humans, a mutation in this gene has been associated with a primary immunodeficiency syndrome, and suggests a role for this protein in endosomal biogenesis. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 28956 — RefSeq curated summary.

At a glance

• Gene–disease (curated): primary immunodeficiency syndrome due to p14 deficiency (Moderate, GenCC)
• GWAS associations: 6
• Clinical variants (ClinVar): 85 total
• Phenotypes (HPO): 10
• Cancer dependency (DepMap): dependent in 61.7% of screened cell lines
• MANE Select transcript: NM_014017

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29796
Approved symbol	LAMTOR2
Name	late endosomal/lysosomal adaptor, MAPK and MTOR activator 2
Location	1q22
Locus type	gene with protein product
Status	Approved
Aliases	MAPBPIP, MAPKSP1AP, p14, ENDAP, Ragulator2
Ensembl gene	ENSG00000116586
Ensembl biotype	protein_coding
OMIM	610389
Entrez	28956

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 8 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000368302, ENST00000368304, ENST00000368305, ENST00000463371, ENST00000487106, ENST00000489664, ENST00000871951, ENST00000871952, ENST00000926593, ENST00000926594, ENST00000926595

RefSeq mRNA: 2 — MANE Select: NM_014017 NM_001145264, NM_014017

CCDS: CCDS1128, CCDS44243

Canonical transcript exons

ENST00000368305 — 4 exons

Exon	Start	End
ENSE00000961270	156055263	156055425
ENSE00001446817	156054782	156054957
ENSE00003494567	156057978	156058067
ENSE00003639829	156058315	156058506

Expression profiles

Bgee: expression breadth ubiquitous, 267 present calls, max score 97.45.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 69.1012 / max 372.2361, expressed in 1827 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
5655	66.4498	1827
5654	2.6103	1407
5653	0.0410	13

Top tissues by expression

284 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	97.45	gold quality
granulocyte	CL:0000094	97.44	gold quality
right lobe of liver	UBERON:0001114	97.43	gold quality
apex of heart	UBERON:0002098	97.43	gold quality
monocyte	CL:0000576	96.92	gold quality
right adrenal gland	UBERON:0001233	96.80	gold quality
leukocyte	CL:0000738	96.75	gold quality
mononuclear cell	CL:0000842	96.73	gold quality
left adrenal gland	UBERON:0001234	96.63	gold quality
left adrenal gland cortex	UBERON:0035825	96.62	gold quality
right adrenal gland cortex	UBERON:0035827	96.60	gold quality
body of stomach	UBERON:0001161	96.43	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	96.20	gold quality
stromal cell of endometrium	CL:0002255	96.12	gold quality
body of pancreas	UBERON:0001150	96.07	gold quality
left coronary artery	UBERON:0001626	95.98	gold quality
lower esophagus mucosa	UBERON:0035834	95.75	gold quality
adrenal cortex	UBERON:0001235	95.64	gold quality
right atrium auricular region	UBERON:0006631	95.64	gold quality
anterior cingulate cortex	UBERON:0009835	95.62	gold quality
hindlimb stylopod muscle	UBERON:0004252	95.60	gold quality
cingulate cortex	UBERON:0003027	95.57	gold quality
muscle layer of sigmoid colon	UBERON:0035805	95.53	gold quality
transverse colon	UBERON:0001157	95.48	gold quality
metanephros cortex	UBERON:0010533	95.46	gold quality
lower esophagus	UBERON:0013473	95.43	gold quality
lower esophagus muscularis layer	UBERON:0035833	95.42	gold quality
coronary artery	UBERON:0001621	95.37	gold quality
rectum	UBERON:0001052	95.35	gold quality
omental fat pad	UBERON:0010414	95.32	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-6701	yes	43.35
E-MTAB-10042	yes	16.50
E-ANND-3	yes	15.05

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

3 targeting LAMTOR2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-6887-3P	99.66	67.83	1778

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 61.7% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 6)

• A complex encoded by the MAPKSP1, ROBLD3, and c11orf59 genes interacts with the Rag GTPases, recruits them to lysosomes, and is essential for mTORC1 activation (PMID:20381137)
• simulations constitute a multi-dimensional exploration of how EGF-dependent EGFR endocytosis and ERK activation are dynamically affected by scaffolds KSR and MP1, co-regulated by Cbl-CIN85 and Endophilin A1 (PMID:21829671)
• The ROBLD3 C-A, thorn23 mutation creates a 50SS capable of recruiting an inhibitory U1 snRNP complex leading to a failure of proper 30 end formation and rapid degradation of p14 mRNA. (PMID:22968171)
• identified polymorphisms in LAMTOR2 and LAMTOR3 do not seem to play a relevant role in breast cancer (PMID:23341997)
• In the two wild type (WT) cases, two novel alterations were detected: a complex deletion of APC and a pathogenic mutation of LAMTOR2. Focusing on WT DT subtype, deep sequencing of CTNNB1, APC and LAMTOR2 was conducted on a retrospective series of 11 WT DT using a targeted approach (PMID:29901254)
• VSIG2 promotes malignant progression of pancreatic ductal adenocarcinoma by enhancing LAMTOR2-mediated mTOR activation. (PMID:37626304)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	lamtor2	ENSDARG00000039872
mus_musculus	Lamtor2	ENSMUSG00000028062
rattus_norvegicus	Lamtor2	ENSRNOG00000019908
drosophila_melanogaster	Lamtor2	FBGN0034350
caenorhabditis_elegans		WBGENE00022402

Protein

Protein identifiers

Ragulator complex protein LAMTOR2 — Q9Y2Q5 (reviewed: Q9Y2Q5)

Alternative names: Endosomal adaptor protein p14, Late endosomal/lysosomal Mp1-interacting protein, Late endosomal/lysosomal adaptor and MAPK and MTOR activator 2, Mitogen-activated protein-binding protein-interacting protein, Roadblock domain-containing protein 3

All UniProt accessions (1): Q9Y2Q5

UniProt curated annotations — full annotation on UniProt →

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 plays a dual role for the small GTPases Rag (RagA/RRAGA, RagB/RRAGB, RagC/RRAGC and/or RagD/RRAGD): it (1) acts as a guanine nucleotide exchange factor (GEF), activating the small GTPases Rag and (2) mediates recruitment of Rag GTPases to the lysosome membrane. 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.

Subunit / interactions. Part of the Ragulator complex composed of LAMTOR1, LAMTOR2, LAMTOR3, LAMTOR4 and LAMTOR5. LAMTOR4 and LAMTOR5 form a heterodimer that interacts, through LAMTOR1, with a LAMTOR2, LAMTOR3 heterodimer. Interacts with LAMTOR1 and LAMTOR3; the interaction is direct. The Ragulator complex interacts with both the mTORC1 complex and heterodimers constituted of the Rag GTPases RagA/RRAGA, RagB/RRAGB, RagC/RRAGC and RagD/RRAGD; regulated by amino acid availability. The Ragulator complex interacts with SLC38A9; the probable amino acid sensor. Interacts with MAPK1 and MAP2K1. Component of the lysosomal folliculin complex (LFC), composed of FLCN, FNIP1 (or FNIP2), RagA/RRAGA or RagB/RRAGB GDP-bound, RagC/RRAGC or RagD/RRAGD GTP-bound, and Ragulator.

Subcellular location. Late endosome membrane. Lysosome membrane.

Disease relevance. Immunodeficiency due to defect in MAPBP-interacting protein (ID-MAPBPIP) [MIM:610798] This form of primary immunodeficiency syndrome includes congenital neutropenia, partial albinism, short stature and B-cell and cytotoxic T-cell deficiency. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the GAMAD family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9Y2Q5-1	1	yes
Q9Y2Q5-2	2
Q9Y2Q5-3	3

RefSeq proteins (2): NP_001138736, NP_054736* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004942	Roadblock/LAMTOR2_dom	Domain
IPR037587	LAMTOR2-like	Family

Pfam: PF03259

UniProt features (19 total): strand 9, helix 3, splice variant 2, mutagenesis site 2, chain 1, region of interest 1, turn 1

Structure

Experimental structures (PDB)

22 structures.

PDB	Method	Resolution (Å)
6B9X	X-RAY DIFFRACTION	1.42
5X6V	X-RAY DIFFRACTION	2.02
6EHP	X-RAY DIFFRACTION	2.3
5X6U	X-RAY DIFFRACTION	2.4
5Y39	X-RAY DIFFRACTION	2.65
6EHR	X-RAY DIFFRACTION	2.9
5Y3A	X-RAY DIFFRACTION	2.9
7UX2	ELECTRON MICROSCOPY	2.9
5YK3	X-RAY DIFFRACTION	3.01
6U62	ELECTRON MICROSCOPY	3.18
6WJ2	ELECTRON MICROSCOPY	3.2
7UXC	ELECTRON MICROSCOPY	3.2
7UXH	ELECTRON MICROSCOPY	3.2
9ED4	ELECTRON MICROSCOPY	3.23
6ULG	ELECTRON MICROSCOPY	3.31
8DHB	ELECTRON MICROSCOPY	3.53
6NZD	ELECTRON MICROSCOPY	3.6
6WJ3	ELECTRON MICROSCOPY	3.9
7T3B	ELECTRON MICROSCOPY	3.9
9ED6	ELECTRON MICROSCOPY	3.98
7T3A	ELECTRON MICROSCOPY	4
7T3C	ELECTRON MICROSCOPY	4

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y2Q5-F1	91.40	0.77

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Mutagenesis-validated functional residues (2):

Position	Phenotype
41–43	in m6 mutant; impaired assembly of the ragulator complex.
44–47	in m7 mutant; impaired association with rag gtpases.

Function

Pathways and Gene Ontology

Reactome pathways

26 pathways

ID	Pathway
R-HSA-1632852	Macroautophagy
R-HSA-165159	MTOR signalling
R-HSA-166208	mTORC1-mediated signalling
R-HSA-380972	Energy dependent regulation of mTOR by LKB1-AMPK
R-HSA-5628897	TP53 Regulates Metabolic Genes
R-HSA-5674135	MAP2K and MAPK activation
R-HSA-6798695	Neutrophil degranulation
R-HSA-8943724	Regulation of PTEN gene transcription
R-HSA-9639288	Amino acids regulate mTORC1
R-HSA-1257604	PIP3 activates AKT signaling
R-HSA-162582	Signal Transduction
R-HSA-168249	Innate Immune System
R-HSA-168256	Immune System
R-HSA-212436	Generic Transcription Pathway
R-HSA-2262752	Cellular responses to stress
R-HSA-3700989	Transcriptional Regulation by TP53
R-HSA-5673001	RAF/MAP kinase cascade
R-HSA-5683057	MAPK family signaling cascades
R-HSA-5684996	MAPK1/MAPK3 signaling
R-HSA-6807070	PTEN Regulation
R-HSA-73857	RNA Polymerase II Transcription
R-HSA-74160	Gene expression (Transcription)
R-HSA-8953897	Cellular responses to stimuli
R-HSA-9006925	Intracellular signaling by second messengers
R-HSA-9612973	Autophagy
R-HSA-9711097	Cellular response to starvation

MSigDB gene sets: 190 (showing top): REACTOME_INNATE_IMMUNE_SYSTEM, GOBP_RESPONSE_TO_ACID_CHEMICAL, GOCC_VACUOLAR_MEMBRANE, GOCC_SECRETORY_GRANULE, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOBP_POSITIVE_REGULATION_OF_TOR_SIGNALING, GOBP_GROWTH, GOBP_POSITIVE_REGULATION_OF_MAPK_CASCADE, AACYNNNNTTCCS_UNKNOWN, TAL1ALPHAE47_01, GOBP_CELLULAR_RESPONSE_TO_ACID_CHEMICAL, GOBP_AMEBOIDAL_TYPE_CELL_MIGRATION, GOBP_CELL_JUNCTION_ORGANIZATION, ONKEN_UVEAL_MELANOMA_UP, KESHELAVA_MULTIPLE_DRUG_RESISTANCE

GO Biological Process (11): regulation of cell growth (GO:0001558), intracellular protein localization (GO:0008104), fibroblast migration (GO:0010761), positive regulation of TOR signaling (GO:0032008), TORC1 signaling (GO:0038202), positive regulation of MAPK cascade (GO:0043410), cellular response to amino acid stimulus (GO:0071230), regulation of cell-substrate junction organization (GO:0150116), protein localization to cell junction (GO:1902414), positive regulation of TORC1 signaling (GO:1904263), positive regulation of intracellular signal transduction (GO:1902533)

GO Molecular Function (3): guanyl-nucleotide exchange factor activity (GO:0005085), molecular adaptor activity (GO:0060090), protein binding (GO:0005515)

GO Cellular Component (13): lysosomal membrane (GO:0005765), late endosome (GO:0005770), plasma membrane (GO:0005886), endosome membrane (GO:0010008), late endosome membrane (GO:0031902), specific granule membrane (GO:0035579), tertiary granule membrane (GO:0070821), Ragulator complex (GO:0071986), FNIP-folliculin RagC/D GAP (GO:1990877), cytoplasm (GO:0005737), lysosome (GO:0005764), endosome (GO:0005768), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-16 pathways:

Category	Pathways
Signal Transduction	2
MTOR signalling	2
Autophagy	1
Transcriptional Regulation by TP53	1
RAF/MAP kinase cascade	1
Innate Immune System	1
PTEN Regulation	1
Cellular response to starvation	1
Intracellular signaling by second messengers	1
Immune System	1
RNA Polymerase II Transcription	1
Cellular responses to stimuli	1
Generic Transcription Pathway	1
MAPK1/MAPK3 signaling	1
MAPK family signaling cascades	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of cellular component organization	2
TOR signaling	2
positive regulation of intracellular signal transduction	2
binding	2
endosome	2
secretory granule membrane	2
cellular anatomical structure	2
cell growth	1
regulation of growth	1
macromolecule localization	1
ameboidal-type cell migration	1
regulation of TOR signaling	1
MAPK cascade	1
regulation of MAPK cascade	1
response to amino acid	1
cellular response to acid chemical	1
cell-substrate junction organization	1
intracellular protein localization	1
positive regulation of TOR signaling	1
TORC1 signaling	1
regulation of TORC1 signaling	1
positive regulation of signal transduction	1
intracellular signal transduction	1
regulation of intracellular signal transduction	1
GTP binding	1
GDP binding	1
GTPase regulator activity	1
molecular_function	1
lysosome	1
lytic vacuole membrane	1
membrane	1
cell periphery	1
cytoplasmic vesicle membrane	1
bounding membrane of organelle	1
late endosome	1
endosome membrane	1
specific granule	1
tertiary granule	1
vacuolar membrane	1
guanyl-nucleotide exchange factor complex	1

Protein interactions and networks

STRING

1478 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LAMTOR2	LAMTOR3	Q9UHA4	999
LAMTOR2	LAMTOR1	Q6IAA8	997
LAMTOR2	LAMTOR4	Q0VGL1	996
LAMTOR2	LAMTOR5	O43504	995
LAMTOR2	RRAGC	Q9HB90	837
LAMTOR2	MAP2K1	Q02750	731
LAMTOR2	RRAGA	Q7L523	714
LAMTOR2	RRAGB	Q5VZM2	686
LAMTOR2	SLC38A9	Q8NBW4	655
LAMTOR2	NPRL2	Q8WTW4	654
LAMTOR2	ARL8B	Q9NVJ2	623
LAMTOR2	RRAGD	Q9NQL2	595
LAMTOR2	NPRL3	Q12980	578
LAMTOR2	MAPK3	P27361	549
LAMTOR2	FLCN	Q8NFG4	496

IntAct

129 interactions, top by confidence:

A	B	Type	Score
LAMTOR3	LAMTOR2	psi-mi:“MI:0915”(physical association)	0.960
LAMTOR2	LAMTOR3	psi-mi:“MI:0915”(physical association)	0.960
LAMTOR3	LAMTOR2	psi-mi:“MI:2364”(proximity)	0.960
LAMTOR2	LAMTOR3	psi-mi:“MI:2364”(proximity)	0.960
LAMTOR4	LAMTOR5	psi-mi:“MI:0914”(association)	0.960
LAMTOR5	LAMTOR4	psi-mi:“MI:0914”(association)	0.960

BioGRID (174): LAMTOR2 (Two-hybrid), LAMTOR2 (Affinity Capture-MS), LAMTOR2 (Affinity Capture-MS), LAMTOR2 (Affinity Capture-Western), LAMTOR3 (Affinity Capture-Western), LAMTOR1 (Affinity Capture-Western), RRAGB (Affinity Capture-Western), RRAGD (Affinity Capture-Western), MTOR (Affinity Capture-Western), RPTOR (Affinity Capture-Western), RRAGA (Affinity Capture-Western), RRAGC (Affinity Capture-Western), LAMTOR2 (Affinity Capture-Western), LAMTOR2 (Affinity Capture-MS), LAMTOR3 (Two-hybrid)

ESM2 similar proteins: A0JN27, A6H7F7, B2RYU6, B5FXJ6, B5FYY5, B5X7X4, B5XGE7, O43504, P55168, P61201, P61202, P61203, P79101, Q05048, Q13888, Q28F72, Q2TBL9, Q2TBV5, Q2YDH6, Q3T132, Q4KLA0, Q4R9A8, Q4VC33, Q5BJQ6, Q5F398, Q5M8X5, Q5R532, Q5R8K2, Q5R9J9, Q5RKJ1, Q63ZJ2, Q6DEG4, Q6DF40, Q6GR10, Q6IQT4, Q6IR75, Q6P1K8, Q7L5Y9, Q7SXR3, Q7ZXB7

Diamond homologs: B5FYY5, B5X7X4, Q3T132, Q63ZJ2, Q6DEG4, Q6DF40, Q7ZXB7, Q9JHS3, Q9N2U6, Q9V8I2, Q9Y2Q5

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
LAMTOR2	“form complex”	LAMTOR	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 63 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
mTORC1-mediated signalling	10	99.1×	4e-16
Energy dependent regulation of mTOR by LKB1-AMPK	10	82.0×	2e-15
MTOR signalling	10	55.3×	9e-14
PTEN Regulation	10	47.6×	3e-13
Amino acids regulate mTORC1	11	45.9×	4e-14
Regulation of PTEN gene transcription	11	40.9×	9e-14
Cellular response to starvation	10	34.5×	7e-12
Autophagy	11	34.0×	5e-13

GO biological processes:

GO term	Partners	Fold	FDR
TORC1 signaling	5	70.4×	9e-07
positive regulation of TOR signaling	8	69.6×	3e-11
cellular response to amino acid stimulus	10	53.8×	8e-13
positive regulation of TORC1 signaling	10	51.9×	8e-13
lysosome localization	5	46.2×	7e-06
negative regulation of autophagy	5	22.7×	2e-04
cellular response to starvation	5	17.0×	5e-04
intracellular protein localization	6	11.0×	6e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

85 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	43
Likely benign	36
Benign	3

Top pathogenic / likely-pathogenic (0)

SpliceAI

434 predictions. Top by Δscore:

Variant	Effect	Δscore
1:156054958:G:GG	donor_gain	1.0000
1:156057975:CAG:C	acceptor_loss	1.0000
1:156057976:AGGAG:A	acceptor_gain	1.0000
1:156057977:GGA:G	acceptor_gain	1.0000
1:156057977:GGAGG:G	acceptor_gain	1.0000
1:156054815:G:GT	donor_gain	0.9900
1:156054815:G:T	donor_gain	0.9900
1:156054873:GGT:G	donor_gain	0.9900
1:156054954:CCCT:C	donor_gain	0.9900
1:156055250:C:CA	acceptor_gain	0.9900
1:156055257:CACCA:C	acceptor_loss	0.9900
1:156055258:ACCAG:A	acceptor_gain	0.9900
1:156055259:CCA:C	acceptor_loss	0.9900
1:156055260:CA:C	acceptor_loss	0.9900
1:156055261:A:AG	acceptor_gain	0.9900
1:156055261:A:T	acceptor_loss	0.9900
1:156055261:AG:A	acceptor_gain	0.9900
1:156055262:G:A	acceptor_loss	0.9900
1:156055262:G:GA	acceptor_gain	0.9900
1:156055262:GG:G	acceptor_gain	0.9900
1:156055262:GGCT:G	acceptor_gain	0.9900
1:156055390:G:GT	donor_gain	0.9900
1:156055421:GCATG:G	donor_gain	0.9900
1:156055426:G:GA	donor_loss	0.9900
1:156055426:G:GG	donor_gain	0.9900
1:156055427:T:G	donor_loss	0.9900
1:156055437:G:T	donor_gain	0.9900
1:156057976:AG:A	acceptor_gain	0.9900
1:156057977:GG:G	acceptor_gain	0.9900
1:156058311:GCAG:G	acceptor_loss	0.9900

AlphaMissense

802 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:156055279:G:A	G29R	1.000
1:156055279:G:C	G29R	1.000
1:156055280:G:A	G29E	1.000
1:156055330:G:C	A46P	1.000
1:156055331:C:A	A46D	1.000
1:156055334:C:A	A47D	1.000
1:156055337:T:A	I48K	1.000
1:156055340:C:A	A49D	1.000
1:156055351:T:A	W53R	1.000
1:156055351:T:C	W53R	1.000
1:156058051:G:A	G102E	1.000
1:156058057:T:A	L104H	1.000
1:156054909:T:C	L7S	0.999
1:156054921:T:A	L11Q	0.999
1:156054921:T:C	L11P	0.999
1:156054957:T:C	L23P	0.999
1:156055265:T:A	L24Q	0.999
1:156055265:T:C	L24P	0.999
1:156055268:T:C	L25P	0.999
1:156055280:G:T	G29V	0.999
1:156055291:G:C	A33P	0.999
1:156055292:C:A	A33D	0.999
1:156055300:G:C	G36R	0.999
1:156055333:G:C	A47P	0.999
1:156055337:T:G	I48R	0.999
1:156055339:G:C	A49P	0.999
1:156055353:G:C	W53C	0.999
1:156055353:G:T	W53C	0.999
1:156055412:T:C	L73P	0.999
1:156057981:G:C	G79R	0.999

dbSNP variants (sampled 300 via entrez): RS1000549353 (1:156054436 C>T), RS1000555633 (1:156053153 G>A,T), RS1001408197 (1:156058870 G>A), RS1001460504 (1:156058559 C>A), RS1002009336 (1:156052887 C>A), RS1002332400 (1:156057177 CAAAAAAAAAAAA>C,CA,CAAAA,CAAAAA,CAAAAAAA,CAAAAAAAA,CAAAAAAAAA,CAAAAAAAAAA,CAAAAAAAAAAA,CAAAAAAAAAAAAA,CAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAAAAA), RS1002448282 (1:156056872 C>G), RS1002614436 (1:156056520 A>G), RS1002643921 (1:156056137 G>A), RS1004093210 (1:156057212 G>A,C), RS1004425421 (1:156054001 G>A,C,T), RS1004456502 (1:156053751 C>G), RS1004864326 (1:156053434 G>A,C), RS1005097607 (1:156055660 A>G), RS1005171078 (1:156055169 T>C)

Disease associations

OMIM: gene MIM:610389 | disease phenotypes: MIM:610798

GenCC curated gene-disease

Disease	Classification	Inheritance
primary immunodeficiency syndrome due to p14 deficiency	Moderate	Autosomal recessive

Mondo (1): primary immunodeficiency syndrome due to p14 deficiency (MONDO:0012559)

Orphanet (1): Primary immunodeficiency syndrome due to P14/LAMTOR2 deficiency (Orphanet:90023)

HPO phenotypes

10 total (10 of 10 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000280	Coarse facial features
HP:0001010	Hypopigmentation of the skin
HP:0001875	Decreased total neutrophil count
HP:0002721	Immunodeficiency
HP:0002850	Decreased circulating total IgM
HP:0004322	Short stature
HP:0005599	Hypopigmentation of hair
HP:0006538	Recurrent bronchopulmonary infections
HP:0007443	Partial albinism

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST007294_124	Body fat distribution (trunk fat ratio)	8.000000e-35
GCST007294_3	Body fat distribution (trunk fat ratio)	6.000000e-21
GCST007294_50	Body fat distribution (trunk fat ratio)	1.000000e-15
GCST007295_17	Body fat distribution (leg fat ratio)	3.000000e-13
GCST007295_37	Body fat distribution (leg fat ratio)	7.000000e-17
GCST007295_72	Body fat distribution (leg fat ratio)	1.000000e-28

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004341	body fat distribution

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C563663	Immunodeficiency due to Defect in MAPBP-Interacting Protein (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

40 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases expression, increases expression, decreases reaction, increases abundance	5
Valproic Acid	affects expression, increases expression	3
sodium arsenite	decreases expression	2
Cisplatin	affects cotreatment, increases expression, affects expression	2
aristolochic acid I	increases expression	1
ginger extract	decreases expression, decreases reaction, increases abundance	1
2,4,6-tribromophenol	decreases expression	1
triphenyl phosphate	affects expression	1
decabromobiphenyl ether	decreases expression	1
arsenite	affects binding, increases reaction	1
cobaltous chloride	decreases expression	1
tetrabromobisphenol A	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
chloropicrin	decreases expression	1
K 7174	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
ICG 001	increases expression	1
bisphenol B	increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
hexabrominated diphenyl ether 153	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
LDN 193189	affects cotreatment, increases expression	1
(+)-JQ1 compound	decreases expression	1
Decitabine	affects expression	1
Diethylhexyl Phthalate	decreases expression	1
Doxorubicin	increases expression	1
Ivermectin	decreases expression	1
Methyl Methanesulfonate	increases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B1VM	Abcam HeLa LAMTOR2 KO	Cancer cell line	Female
CVCL_E1N2	HyCyte THP-1 KO-hLAMTOR2	Cancer cell line	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.