LAMTOR4

Summary

LAMTOR4 (late endosomal/lysosomal adaptor, MAPK and MTOR activator 4, HGNC:33772) is a protein-coding gene on chromosome 7q22.1, encoding Ragulator complex protein LAMTOR4 (Q0VGL1). 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: 53.1% of cell lines).

Contributes to guanyl-nucleotide exchange factor activity and molecular adaptor activity. Involved in several processes, including cellular response to amino acid stimulus; positive regulation of TORC1 signaling; and protein localization to lysosome. Located in lysosome. Part of FNIP-folliculin RagC/D GAP and Ragulator complex. Is active in lysosomal membrane.

Source: NCBI Gene 389541 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 26 total — 1 pathogenic
• Cancer dependency (DepMap): dependent in 53.1% of screened cell lines
• MANE Select transcript: NM_001008395

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33772
Approved symbol	LAMTOR4
Name	late endosomal/lysosomal adaptor, MAPK and MTOR activator 4
Location	7q22.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000188186
Ensembl biotype	protein_coding
OMIM	618834
Entrez	389541

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 9 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000341942, ENST00000441173, ENST00000460732, ENST00000466498, ENST00000468582, ENST00000473459, ENST00000474141, ENST00000474831, ENST00000488241, ENST00000488338, ENST00000490633, ENST00000494136

RefSeq mRNA: 6 — MANE Select: NM_001008395 NM_001008395, NM_001318236, NM_001318237, NM_001394587, NM_001394588, NM_001394589

CCDS: CCDS34702, CCDS83210, CCDS83211

Canonical transcript exons

ENST00000341942 — 4 exons

Exon	Start	End
ENSE00001421647	100148918	100148975
ENSE00003601022	100149499	100149579
ENSE00003672116	100153867	100154203
ENSE00003732821	100153400	100153517

Expression profiles

Bgee: expression breadth ubiquitous, 255 present calls, max score 99.33.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 53.2725 / max 331.4850, expressed in 1826 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
79931	47.4343	1826
79932	5.2924	1584
79933	0.2730	154
79934	0.2023	99
79935	0.0706	27

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
skin of abdomen	UBERON:0001416	99.33	gold quality
mucosa of transverse colon	UBERON:0004991	99.30	gold quality
skin of leg	UBERON:0001511	99.25	gold quality
upper arm skin	UBERON:0004263	99.24	gold quality
granulocyte	CL:0000094	99.17	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	98.84	gold quality
zone of skin	UBERON:0000014	98.80	gold quality
monocyte	CL:0000576	98.79	gold quality
leukocyte	CL:0000738	98.78	gold quality
spleen	UBERON:0002106	98.74	gold quality
adenohypophysis	UBERON:0002196	98.68	gold quality
transverse colon	UBERON:0001157	98.65	gold quality
body of stomach	UBERON:0001161	98.51	gold quality
anterior cingulate cortex	UBERON:0009835	98.49	gold quality
right frontal lobe	UBERON:0002810	98.46	gold quality
apex of heart	UBERON:0002098	98.43	gold quality
Brodmann (1909) area 9	UBERON:0013540	98.43	gold quality
metanephros cortex	UBERON:0010533	98.42	gold quality
right uterine tube	UBERON:0001302	98.40	gold quality
tendon of biceps brachii	UBERON:0008188	98.37	gold quality
right hemisphere of cerebellum	UBERON:0014890	98.37	gold quality
small intestine Peyer’s patch	UBERON:0003454	98.35	gold quality
pituitary gland	UBERON:0000007	98.31	gold quality
hypothalamus	UBERON:0001898	98.31	gold quality
cerebellar hemisphere	UBERON:0002245	98.30	gold quality
muscle layer of sigmoid colon	UBERON:0035805	98.29	gold quality
cerebellar cortex	UBERON:0002129	98.26	gold quality
right lobe of thyroid gland	UBERON:0001119	98.24	gold quality
spinal cord	UBERON:0002240	98.22	gold quality
lymph node	UBERON:0000029	98.21	gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-HCAD-4	yes	207.35
E-HCAD-1	yes	68.79
E-MTAB-6701	yes	29.66
E-MTAB-10042	yes	11.32
E-MTAB-6379	no	468.83
E-MTAB-6524	no	369.32
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting LAMTOR4, 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-497-5P	99.92	71.83	2674
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-4739	99.84	65.25	1832
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-3168	99.08	67.75	1384
HSA-MIR-5001-5P	99.05	66.76	1972
HSA-MIR-499B-5P	98.35	68.39	988
HSA-MIR-4494	97.86	64.93	850
HSA-MIR-6782-5P	96.45	64.42	612
HSA-MIR-3162-5P	95.67	67.53	794
HSA-MIR-1915-5P	95.25	65.78	571

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 53.1% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 4)

• Study identified HBXIP and C7orf59 as two additional Ragulator components that are required for mTORC1 activation by amino acids. (PMID:22980980)
• The C7orf59 was phosphorylated by protein kinase A (PKA) in vitro and mutation of the conserved Ser67 residue to aspartate prevented phosphorylation and negatively affected the C7orf59 interaction with p18 both in cell culture and in vitro. (PMID:31314152)
• Lysosomal TMEM9-LAMTOR4-controlled mTOR signaling integrity is required for mammary tumorigenesis. (PMID:36336962)
• Elevated LAMTOR4 Expression Is Associated with Lethal Prostate Cancer and Its Knockdown Decreases Cell Proliferation, Invasion, and Migration In Vitro. (PMID:39125671)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	lamtor4	ENSDARG00000045542
mus_musculus	Lamtor4	ENSMUSG00000050552
rattus_norvegicus	Lamtor4	ENSRNOG00000027028
drosophila_melanogaster	Lamtor4	FBGN0035469

Protein

Protein identifiers

Ragulator complex protein LAMTOR4 — Q0VGL1 (reviewed: Q0VGL1)

Alternative names: Late endosomal/lysosomal adaptor and MAPK and MTOR activator 4

All UniProt accessions (8): A0A087WT92, A0A087WV46, A0A087WVK8, A0A087WVU0, A0A087WWR0, A0A087WXQ3, C9JXA7, Q0VGL1

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.

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. 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. 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. Lysosome.

Post-translational modifications. Phosphorylation at Ser-67 by PKA inhibits Ragulator complex assembly.

Similarity. Belongs to the LAMTOR4 family.

RefSeq proteins (6): NP_001008396, NP_001305165, NP_001305166, NP_001381516, NP_001381517, NP_001381518 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR034601	LAMTOR4	Family

UniProt features (19 total): strand 7, modified residue 3, mutagenesis site 3, chain 2, helix 2, initiator methionine 1, turn 1

Structure

Experimental structures (PDB)

25 structures.

PDB	Method	Resolution (Å)
6B9X	X-RAY DIFFRACTION	1.42
5X6V	X-RAY DIFFRACTION	2.02
5YK5	X-RAY DIFFRACTION	2.03
6EHP	X-RAY DIFFRACTION	2.3
5X6U	X-RAY DIFFRACTION	2.4
5Y39	X-RAY DIFFRACTION	2.65
5Y38	X-RAY DIFFRACTION	2.8
5VOK	X-RAY DIFFRACTION	2.89
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-Q0VGL1-F1	87.65	0.67

Functional residue map

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

Post-translational modifications (3): 1, 2, 67

Mutagenesis-validated functional residues (3):

Position	Phenotype
34–35	does not affect ragulator complex assembly.
36–37	does not affect ragulator complex assembly.
67	mimics phosphorylation; inhibiting ragulator complex assembly.

Function

Pathways and Gene Ontology

Reactome pathways

19 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-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-212436	Generic Transcription Pathway
R-HSA-2262752	Cellular responses to stress
R-HSA-3700989	Transcriptional Regulation by TP53
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: 143 (showing top): GOBP_RESPONSE_TO_ACID_CHEMICAL, GOCC_VACUOLAR_MEMBRANE, GOBP_POSITIVE_REGULATION_OF_TOR_SIGNALING, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_CELLULAR_RESPONSE_TO_ACID_CHEMICAL, GOBP_PROTEIN_LOCALIZATION_TO_LYSOSOME, GOBP_REGULATION_OF_ANATOMICAL_STRUCTURE_SIZE, GOBP_PROTEIN_LOCALIZATION_TO_VACUOLE, GOBP_REGULATION_OF_CELL_SIZE, GOBP_POSITIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_TOR_SIGNALING, GOCC_LATE_ENDOSOME_MEMBRANE, GOMF_GUANYL_NUCLEOTIDE_EXCHANGE_FACTOR_ACTIVITY

GO Biological Process (6): regulation of cell size (GO:0008361), positive regulation of TOR signaling (GO:0032008), TORC1 signaling (GO:0038202), protein localization to lysosome (GO:0061462), cellular response to amino acid stimulus (GO:0071230), positive regulation of TORC1 signaling (GO:1904263)

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

GO Cellular Component (5): lysosome (GO:0005764), lysosomal membrane (GO:0005765), late endosome membrane (GO:0031902), Ragulator complex (GO:0071986), FNIP-folliculin RagC/D GAP (GO:1990877)

Reactome top-level categories

Rollup of top-13 pathways:

Category	Pathways
Signal Transduction	2
MTOR signalling	2
Autophagy	1
Transcriptional Regulation by TP53	1
PTEN Regulation	1
Cellular response to starvation	1
Intracellular signaling by second messengers	1
RNA Polymerase II Transcription	1
Cellular responses to stimuli	1
Generic Transcription Pathway	1
PIP3 activates AKT signaling	1
Gene expression (Transcription)	1
Cellular responses to stress	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
TOR signaling	2
binding	2
regulation of cellular component size	1
regulation of TOR signaling	1
positive regulation of intracellular signal transduction	1
protein localization to vacuole	1
response to amino acid	1
cellular response to acid chemical	1
positive regulation of TOR signaling	1
TORC1 signaling	1
regulation of TORC1 signaling	1
GTP binding	1
GDP binding	1
GTPase regulator activity	1
molecular_function	1
lytic vacuole	1
lysosome	1
lytic vacuole membrane	1
late endosome	1
endosome membrane	1
vacuolar membrane	1
guanyl-nucleotide exchange factor complex	1
membrane protein complex	1
GTPase activator complex	1

Protein interactions and networks

STRING

768 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LAMTOR4	LAMTOR5	O43504	996
LAMTOR4	LAMTOR1	Q6IAA8	996
LAMTOR4	LAMTOR3	Q9UHA4	996
LAMTOR4	LAMTOR2	Q9Y2Q5	996
LAMTOR4	RRAGA	Q7L523	794
LAMTOR4	SLC38A9	Q8NBW4	760
LAMTOR4	RRAGC	Q9HB90	720
LAMTOR4	EFNA5	P52803	700
LAMTOR4	RRAGB	Q5VZM2	674
LAMTOR4	NPRL2	Q8WTW4	644
LAMTOR4	RRAGD	Q9NQL2	602
LAMTOR4	WDR24	Q96S15	571
LAMTOR4	WDR59	Q6PJI9	570
LAMTOR4	RHEB	Q15382	570
LAMTOR4	MIOS	Q9NXC5	540

IntAct

77 interactions, top by confidence:

A	B	Type	Score
LAMTOR4	LAMTOR5	psi-mi:“MI:0915”(physical association)	0.960
LAMTOR4	LAMTOR5	psi-mi:“MI:0407”(direct interaction)	0.960
LAMTOR5	LAMTOR4	psi-mi:“MI:0915”(physical association)	0.960
LAMTOR4	LAMTOR5	psi-mi:“MI:0914”(association)	0.960
LAMTOR5	LAMTOR4	psi-mi:“MI:0914”(association)	0.960
LAMTOR4	LAMTOR1	psi-mi:“MI:2364”(proximity)	0.910
LAMTOR1	LAMTOR4	psi-mi:“MI:0915”(physical association)	0.910
LAMTOR4	LAMTOR1	psi-mi:“MI:0914”(association)	0.910
LAMTOR1	LAMTOR4	psi-mi:“MI:0403”(colocalization)	0.910
LAMTOR1	LAMTOR5	psi-mi:“MI:0915”(physical association)	0.870
LAMTOR1	LAMTOR5	psi-mi:“MI:0914”(association)	0.870
LAMTOR2	LAMTOR5	psi-mi:“MI:0914”(association)	0.860

BioGRID (86): LAMTOR4 (Two-hybrid), LAMTOR4 (Affinity Capture-MS), LAMTOR4 (Affinity Capture-MS), LAMTOR4 (Affinity Capture-MS), LAMTOR4 (Affinity Capture-MS), LAMTOR4 (Affinity Capture-MS), LAMTOR4 (Affinity Capture-MS), LAMTOR4 (Affinity Capture-MS), LAMTOR4 (Affinity Capture-MS), LAMTOR4 (Affinity Capture-MS), LAMTOR4 (Affinity Capture-MS), SLC38A9 (Affinity Capture-MS), LAMTOR4 (Affinity Capture-MS), LAMTOR4 (Two-hybrid), LAMTOR4 (Two-hybrid)

ESM2 similar proteins: A4GCR5, A4GCR7, A4GCR8, A4GD50, A4GD54, A4GDQ8, A4GDR9, A4GDT3, A4GE38, A4GE39, A4KA54, A4KA61, A7RT29, A7S6M8, A9UMU8, D3ZVF4, P02584, P06625, P07737, P08240, P35080, P38334, P62962, P62963, Q08CN0, Q09430, Q0P3X8, Q0VGL1, Q29EZ6, Q29NZ8, Q2M2U3, Q2NKT1, Q3MHE8, Q4PM15, Q4R4P8, Q4S4I5, Q54DY3, Q54QW5, Q5IRJ7, Q5R483

Diamond homologs: A7S6M8, A9UMU8, Q0P3X8, Q0VGL1, Q29EZ6, Q2M2U3, Q5R483, Q8CF66, Q9VZL6, Q54DY3

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
LAMTOR4	“form complex”	LAMTOR	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 46 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	9	115.7×	5e-15
Energy dependent regulation of mTOR by LKB1-AMPK	9	95.8×	2e-14
MTOR signalling	9	64.6×	5e-13
PTEN Regulation	9	55.6×	1e-12
Amino acids regulate mTORC1	9	48.7×	4e-12
Regulation of PTEN gene transcription	10	48.2×	4e-13
Cellular response to starvation	9	40.3×	2e-11
Autophagy	10	40.1×	1e-12

GO biological processes:

GO term	Partners	Fold	FDR
TORC1 signaling	5	97.9×	1e-07
positive regulation of TOR signaling	7	84.6×	2e-10
cellular response to amino acid stimulus	9	67.3×	3e-12
positive regulation of TORC1 signaling	8	57.7×	2e-10
intracellular protein localization	7	17.9×	9e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	20
Likely benign	0
Benign	2

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
2579262	GRCh38/hg38 7q22.1(chr7:98454022-100723798)x1	Pathogenic

SpliceAI

1220 predictions. Top by Δscore:

Variant	Effect	Δscore
7:100153387:C:A	acceptor_gain	1.0000
7:100153391:T:TA	acceptor_gain	1.0000
7:100153394:A:AG	acceptor_gain	1.0000
7:100153394:AT:A	acceptor_gain	1.0000
7:100153395:T:G	acceptor_gain	1.0000
7:100153396:GCAGT:G	acceptor_loss	1.0000
7:100153398:AGT:A	acceptor_loss	1.0000
7:100153399:GT:G	acceptor_gain	1.0000
7:100153399:GTC:G	acceptor_gain	1.0000
7:100153399:GTCAT:G	acceptor_gain	1.0000
7:100155256:CTGTA:C	donor_loss	1.0000
7:100155257:TGTA:T	donor_loss	1.0000
7:100155258:GTAC:G	donor_loss	1.0000
7:100155259:TAC:T	donor_loss	1.0000
7:100155260:A:AC	donor_gain	1.0000
7:100155261:C:A	donor_loss	1.0000
7:100155261:C:CC	donor_gain	1.0000
7:100155261:CCT:C	donor_gain	1.0000
7:100155451:CTTAG:C	acceptor_gain	1.0000
7:100155452:TTAG:T	acceptor_gain	1.0000
7:100155453:TAG:T	acceptor_gain	1.0000
7:100155454:AG:A	acceptor_gain	1.0000
7:100155456:C:CC	acceptor_gain	1.0000
7:100155457:T:C	acceptor_loss	1.0000
7:100155666:CCCA:C	donor_loss	1.0000
7:100155667:CCAC:C	donor_loss	1.0000
7:100155668:CAC:C	donor_loss	1.0000
7:100155669:A:C	donor_loss	1.0000
7:100155685:T:TA	donor_gain	1.0000
7:100155686:C:A	donor_gain	1.0000

AlphaMissense

620 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:100149544:G:C	G17R	0.999
7:100149545:G:A	G17D	0.999
7:100149545:G:T	G17V	0.999
7:100149551:T:C	L19P	0.999
7:100153406:G:T	G31W	0.999
7:100153407:G:A	G31E	0.999
7:100153407:G:T	G31V	0.999
7:100153413:T:C	L33P	0.999
7:100149544:G:T	G17C	0.998
7:100153406:G:A	G31R	0.998
7:100153406:G:C	G31R	0.998
7:100153452:T:C	L46P	0.998
7:100153917:T:C	F85L	0.998
7:100153919:T:A	F85L	0.998
7:100153919:T:G	F85L	0.998
7:100153921:T:A	V86E	0.998
7:100153928:G:C	K88N	0.998
7:100153928:G:T	K88N	0.998
7:100149544:G:A	G17S	0.997
7:100153420:T:A	N35K	0.997
7:100153420:T:G	N35K	0.997
7:100153434:C:A	A40D	0.997
7:100153455:T:A	V47D	0.997
7:100153464:C:A	A50D	0.997
7:100153512:T:C	L66P	0.997
7:100149572:T:A	V26E	0.996
7:100149577:G:C	A28P	0.996
7:100153400:T:C	S29P	0.996
7:100153897:C:A	T78K	0.996
7:100153918:T:C	F85S	0.996

dbSNP variants (sampled 300 via entrez): RS1000365121 (7:100147660 A>G), RS1001625016 (7:100150520 T>C), RS1001778640 (7:100149738 C>T), RS1001823202 (7:100148836 A>G,T), RS1002427352 (7:100150057 G>A), RS1002854997 (7:100152083 C>G), RS1002896036 (7:100148996 G>A,C), RS1003191180 (7:100147976 A>G), RS1003639937 (7:100148227 A>G,T), RS1003686002 (7:100153442 A>G,T), RS1003837945 (7:100151853 C>A,T), RS1003923461 (7:100147228 C>G,T), RS1003985598 (7:100154662 C>G), RS1004933908 (7:100148656 G>A,C), RS1005004393 (7:100148418 C>A,G,T)

Disease associations

OMIM: gene MIM:618834 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): multiple congenital anomalies/dysmorphic syndrome (MONDO:0019042)

Orphanet (1): Multiple congenital anomalies/dysmorphic syndrome (Orphanet:68341)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST004068_27	Venous thromboembolism adjusted for sickle cell variant rs77121243-T	6.000000e-06
GCST010002_259	Refractive error	3.000000e-16
GCST010702_48	Subcortical volume (MOSTest)	6.000000e-10
GCST010703_289	Brain morphology (MOSTest)	6.000000e-15

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Particulate Matter	decreases expression, increases abundance, affects cotreatment	3
sodium arsenite	decreases expression, increases expression	2
Air Pollutants	decreases expression, affects expression, increases abundance	2
aristolochic acid I	increases expression	1
triphenyl phosphate	affects expression	1
arsenite	increases reaction, affects binding	1
isobutyl alcohol	affects cotreatment, decreases expression, increases abundance	1
K 7174	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
(+)-JQ1 compound	decreases expression	1
Vehicle Emissions	increases abundance, decreases expression	1
Cadmium	affects expression, affects response to substance	1
Cisplatin	affects cotreatment, increases expression	1
Gasoline	affects cotreatment, decreases expression, increases abundance	1
Ozone	increases abundance, affects expression	1
Polycyclic Aromatic Hydrocarbons	affects cotreatment, decreases expression, increases abundance	1
Thiram	decreases expression	1
Tretinoin	increases expression	1
Cyclosporine	decreases expression	1
Asbestos, Crocidolite	increases expression	1

Cellosaurus cell lines

4 cell lines: 3 cancer cell line, 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B3A0	Abcam HEK293T LAMTOR4 KO	Transformed cell line	Female
CVCL_SV28	HAP1 LAMTOR4 (-) 1	Cancer cell line	Male
CVCL_SV29	HAP1 LAMTOR4 (-) 2	Cancer cell line	Male
CVCL_SV30	HAP1 LAMTOR4 (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

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