MTMR9

Summary

MTMR9 (myotubularin related protein 9, HGNC:14596) is a protein-coding gene on chromosome 8p23.1, encoding Myotubularin-related protein 9 (Q96QG7). Acts as an adapter for myotubularin-related phosphatases.

This gene encodes a myotubularin-related protein that is atypical to most other members of the myotubularin-related protein family because it has no dual-specificity phosphatase domain. The encoded protein contains a double-helical motif similar to the SET interaction domain, which is thought to have a role in the control of cell proliferation. In mouse, a protein similar to the encoded protein binds with MTMR7, and together they dephosphorylate phosphatidylinositol 3-phosphate and inositol 1,3-bisphosphate.

Source: NCBI Gene 66036 — RefSeq curated summary.

At a glance

• GWAS associations: 27
• Clinical variants (ClinVar): 379 total
• MANE Select transcript: NM_015458

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14596
Approved symbol	MTMR9
Name	myotubularin related protein 9
Location	8p23.1
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp434K171, LIP-STYX
Ensembl gene	ENSG00000104643
Ensembl biotype	protein_coding
OMIM	606260
Entrez	66036

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000221086, ENST00000526292, ENST00000528389, ENST00000530200, ENST00000942357

RefSeq mRNA: 1 — MANE Select: NM_015458 NM_015458

CCDS: CCDS5979

Canonical transcript exons

ENST00000221086 — 10 exons

Exon	Start	End
ENSE00001166667	11284816	11285070
ENSE00001189960	11322625	11328146
ENSE00003534747	11316673	11316893
ENSE00003556108	11314923	11315064
ENSE00003556964	11295194	11295302
ENSE00003561129	11309527	11309688
ENSE00003583163	11306190	11306407
ENSE00003630196	11300023	11300148
ENSE00003646125	11304841	11305014
ENSE00003683813	11319687	11319838

Expression profiles

Bgee: expression breadth ubiquitous, 289 present calls, max score 97.63.

FANTOM5 (CAGE): breadth broad, TPM avg 1.9678 / max 36.6681, expressed in 746 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
87378	7.7420	1782
87377	6.4884	1728
199478	1.9678	746
87376	0.5527	267
87379	0.2965	134
87375	0.1345	60

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	97.63	gold quality
Brodmann (1909) area 46	UBERON:0006483	95.06	gold quality
substantia nigra pars compacta	UBERON:0001965	94.36	gold quality
CA1 field of hippocampus	UBERON:0003881	94.16	gold quality
cerebellar vermis	UBERON:0004720	94.02	gold quality
pons	UBERON:0000988	93.77	gold quality
secondary oocyte	CL:0000655	93.75	gold quality
substantia nigra pars reticulata	UBERON:0001966	93.69	gold quality
Brodmann (1909) area 23	UBERON:0013554	93.52	gold quality
middle temporal gyrus	UBERON:0002771	93.14	gold quality
lateral nuclear group of thalamus	UBERON:0002736	92.46	gold quality
parietal lobe	UBERON:0001872	92.05	gold quality
orbitofrontal cortex	UBERON:0004167	91.96	gold quality
superior vestibular nucleus	UBERON:0007227	91.89	gold quality
postcentral gyrus	UBERON:0002581	91.88	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	91.68	gold quality
medulla oblongata	UBERON:0001896	91.45	gold quality
entorhinal cortex	UBERON:0002728	91.43	gold quality
superior frontal gyrus	UBERON:0002661	91.24	gold quality
ventral tegmental area	UBERON:0002691	91.20	gold quality
subthalamic nucleus	UBERON:0001906	90.08	gold quality
inferior olivary complex	UBERON:0002127	90.02	gold quality
inferior vagus X ganglion	UBERON:0005363	89.80	gold quality
cortical plate	UBERON:0005343	89.63	gold quality
dorsal plus ventral thalamus	UBERON:0001897	89.44	gold quality
dorsal root ganglion	UBERON:0000044	89.42	gold quality
choroid plexus epithelium	UBERON:0003911	88.37	gold quality
left ventricle myocardium	UBERON:0006566	88.24	gold quality
lateral globus pallidus	UBERON:0002476	88.14	gold quality
occipital lobe	UBERON:0002021	88.12	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.85

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): STAT1

miRNA regulators (miRDB)

202 targeting MTMR9, 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-4776-3P	100.00	68.73	1340
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-4803	99.98	71.99	3117

Literature-anchored findings (GeneRIF, showing 7)

• Association of single-nucleotide polymorphisms in MTMR9 gene with obesity. (PMID:17855449)
• MTMR9 greatly enhances the functions of MTMR6 (PMID:19038970)
• Our data suggest that genetic variations in the FTO, SCG3 and MTMR9 genes independently influence the risk of metabolic syndrome. (PMID:21796137)
• MTMR6, which dephosphorylates PI(3)P to PI, and its binding partner MTMR9, are required for macropinocytosis. (PMID:24591580)
• Polymorphism of rs2293855 in MTMR9 is associated with measures of glucose tolerance, indices of insulin secretion and indices of insulin sensitivity. (PMID:24937802)
• MTMR9 localizes to the intermediate compartment and to the Golgi apparatus. MTMR9 modulates WNT3A signalling by interfering with WNT3A secretion. (PMID:31704058)
• Genetic Variants of the MTMR9 Gene Are Associated with Nonspecific Intellectual Disability: A Family-Based Association Study. (PMID:32991201)

Cross-species orthologs

15 orthologs

Organism	Symbol	Gene ID
danio_rerio	mtmr9	ENSDARG00000015860
mus_musculus	Mtmr9	ENSMUSG00000035078
rattus_norvegicus	Mtmr9	ENSRNOG00000011560
drosophila_melanogaster	mtm	FBGN0025742
drosophila_melanogaster	Sbf	FBGN0025802
drosophila_melanogaster	Mtmr6	FBGN0028497
drosophila_melanogaster	CG14411	FBGN0030582
drosophila_melanogaster	CG3632	FBGN0030735
drosophila_melanogaster	CG5026	FBGN0035945
caenorhabditis_elegans	mtm-1	WBGENE00003475
caenorhabditis_elegans		WBGENE00003476
caenorhabditis_elegans		WBGENE00003477
caenorhabditis_elegans		WBGENE00003478
caenorhabditis_elegans		WBGENE00003479
caenorhabditis_elegans	mtm-10	WBGENE00021683

Paralogs (13): MTMR7 (ENSG00000003987), MTMR11 (ENSG00000014914), MTMR1 (ENSG00000063601), MTMR2 (ENSG00000087053), SBF1 (ENSG00000100241), MTMR3 (ENSG00000100330), MTMR8 (ENSG00000102043), MTMR4 (ENSG00000108389), SBF2 (ENSG00000133812), MTMR6 (ENSG00000139505), MTMR12 (ENSG00000150712), MTMR10 (ENSG00000166912), MTM1 (ENSG00000171100)

Protein

Protein identifiers

Myotubularin-related protein 9 — Q96QG7 (reviewed: Q96QG7)

Alternative names: Inactive phosphatidylinositol 3-phosphatase 9

All UniProt accessions (2): E9PR67, Q96QG7

UniProt curated annotations — full annotation on UniProt →

Function. Acts as an adapter for myotubularin-related phosphatases. Increases lipid phosphatase MTMR6 catalytic activity, specifically towards phosphatidylinositol 3,5-bisphosphate and MTMR6 binding affinity for phosphorylated phosphatidylinositols. Positively regulates lipid phosphatase MTMR7 catalytic activity. Increases MTMR8 catalytic activity towards phosphatidylinositol 3-phosphate. The formation of the MTMR6-MTMR9 complex, stabilizes both MTMR6 and MTMR9 protein levels. Stabilizes MTMR8 protein levels. Plays a role in the late stages of macropinocytosis possibly by regulating MTMR6-mediated dephosphorylation of phosphatidylinositol 3-phosphate in membrane ruffles. Negatively regulates autophagy, in part via its association with MTMR8. Negatively regulates DNA damage-induced apoptosis, in part via its association with MTMR6. Does not bind mono-, di- and tri-phosphorylated phosphatidylinositols, phosphatidic acid and phosphatidylserine.

Subunit / interactions. Homodimer. Heterodimer (via C-terminus) with lipid phosphatase MTMR6 (via C-terminus). Heterodimer (via coiled coil domain) with lipid phosphatase MTMR7 (via C-terminus). Heterodimer with lipid phosphatase MTMR8.

Subcellular location. Cytoplasm. Cell projection. Ruffle membrane. Perinuclear region. Endoplasmic reticulum.

Tissue specificity. Expressed in many tissues.

Domain organisation. The GRAM domain is required for cell membrane localization. The coiled coil domain mediates interaction with MTMR9.

Similarity. Belongs to the protein-tyrosine phosphatase family. Non-receptor class myotubularin subfamily.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96QG7-1	1	yes
Q96QG7-2	2

RefSeq proteins (1): NP_056273* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010569	Myotubularin-like_Pase_dom	Domain
IPR011993	PH-like_dom_sf	Homologous_superfamily
IPR029021	Prot-tyrosine_phosphatase-like	Homologous_superfamily
IPR030564	Myotubularin	Family
IPR048994	PH-GRAM_MTMR6-9	Domain

Pfam: PF06602, PF21098

UniProt features (10 total): domain 2, modified residue 2, sequence conflict 2, chain 1, coiled-coil region 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96QG7-F1	95.16	0.91

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 (2): 1, 548

Function

Pathways and Gene Ontology

Reactome pathways

8 pathways

ID	Pathway
R-HSA-1660499	Synthesis of PIPs at the plasma membrane
R-HSA-1660517	Synthesis of PIPs at the late endosome membrane
R-HSA-1855183	Synthesis of IP2, IP, and Ins in the cytosol
R-HSA-1430728	Metabolism
R-HSA-1483249	Inositol phosphate metabolism
R-HSA-1483255	PI Metabolism
R-HSA-1483257	Phospholipid metabolism
R-HSA-556833	Metabolism of lipids

MSigDB gene sets: 279 (showing top): GOBP_LIPID_MODIFICATION, GOBP_REGULATION_OF_AUTOPHAGY, GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLINOSITOL_METABOLIC_PROCESS, LU_IL4_SIGNALING, GOBP_REGULATION_OF_PHOSPHATASE_ACTIVITY, GOBP_PHOSPHOLIPID_DEPHOSPHORYLATION, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_VESICLE_MEDIATED_TRANSPORT, GOCC_RUFFLE, GOBP_REGULATION_OF_PHOSPHOLIPID_METABOLIC_PROCESS, GOBP_MACROAUTOPHAGY, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, MODULE_66

GO Biological Process (6): endocytosis (GO:0006897), negative regulation of autophagy (GO:0010507), positive regulation of phosphatase activity (GO:0010922), phosphatidylinositol dephosphorylation (GO:0046856), protein stabilization (GO:0050821), regulation of phosphatidylinositol dephosphorylation (GO:0060304)

GO Molecular Function (3): protein phosphatase binding (GO:0019903), enzyme regulator activity (GO:0030234), protein binding (GO:0005515)

GO Cellular Component (9): cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), cytosol (GO:0005829), ruffle membrane (GO:0032587), protein-containing complex (GO:0032991), perinuclear region of cytoplasm (GO:0048471), plasma membrane (GO:0005886), membrane (GO:0016020), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-5 pathways:

Category	Pathways
PI Metabolism	2
Metabolism	2
Inositol phosphate metabolism	1
Phospholipid metabolism	1
Metabolism of lipids	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
cytoplasm	3
vesicle budding from membrane	1
membrane invagination	1
vesicle-mediated transport	1
import into cell	1
autophagy	1
negative regulation of catabolic process	1
regulation of autophagy	1
regulation of phosphatase activity	1
phosphatase activity	1
positive regulation of dephosphorylation	1
positive regulation of hydrolase activity	1
phosphatidylinositol metabolic process	1
phospholipid dephosphorylation	1
regulation of protein stability	1
regulation of lipid metabolic process	1
regulation of dephosphorylation	1
phosphatidylinositol dephosphorylation	1
regulation of phosphorus metabolic process	1
regulation of macromolecule metabolic process	1
phosphatase binding	1
catalytic activity	1
molecular function regulator activity	1
binding	1
intracellular anatomical structure	1
endomembrane system	1
intracellular membrane-bounded organelle	1
ruffle	1
cell projection membrane	1
leading edge membrane	1
cellular_component	1
membrane	1
cell periphery	1

Protein interactions and networks

STRING

1321 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MTMR9	MTMR6	Q9Y217	905
MTMR9	FAM167A	Q96KS9	871
MTMR9	BLK	P51451	686
MTMR9	XKR6	Q5GH73	649
MTMR9	KRT9	P35527	588
MTMR9	LCA5L	O95447	542
MTMR9	MTMR14	Q8NCE2	515
MTMR9	KRT1	P04264	496
MTMR9	PLPP6	Q8IY26	470
MTMR9	SH3BGR	P55822	434
MTMR9	NEIL2	Q969S2	431
MTMR9	PSMG1	O95456	426
MTMR9	B3GALT5	Q9Y2C3	418
MTMR9	PUDP	Q08623	417
MTMR9	PRAG1	Q86YV5	414

IntAct

138 interactions, top by confidence:

A	B	Type	Score
MTMR7	MTMR9	psi-mi:“MI:0915”(physical association)	0.940
MTMR9	MTMR7	psi-mi:“MI:0915”(physical association)	0.940
MTMR6	MTMR9	psi-mi:“MI:0915”(physical association)	0.920
MTMR9	MTMR6	psi-mi:“MI:0915”(physical association)	0.920
MTMR6	MTMR9	psi-mi:“MI:2364”(proximity)	0.920
MTMR8	MTMR9	psi-mi:“MI:0915”(physical association)	0.890
MTMR9	MTMR8	psi-mi:“MI:0915”(physical association)	0.890
EMILIN1	MTMR9	psi-mi:“MI:0915”(physical association)	0.880
MTMR9	EMILIN1	psi-mi:“MI:0915”(physical association)	0.880

BioGRID (126): MTMR9 (Two-hybrid), MTMR9 (Two-hybrid), MTMR9 (Two-hybrid), MTMR9 (Two-hybrid), MTMR9 (Two-hybrid), MTMR9 (Two-hybrid), MTMR9 (Two-hybrid), LNX1 (Two-hybrid), MTMR9 (Affinity Capture-MS), MTMR9 (Two-hybrid), MTMR9 (Two-hybrid), MTMR9 (Two-hybrid), MTMR9 (Two-hybrid), MTMR9 (Two-hybrid), MTMR9 (Co-fractionation)

ESM2 similar proteins: A0A0G2JXT6, A0JMF6, A0JMK5, A2ALK8, A2BGG1, A6QLT4, A7MB43, G5ED68, O13819, O14830, P26045, P33402, P51432, Q09M05, Q13496, Q13613, Q15111, Q3USB7, Q4KWH5, Q4R6N0, Q4U2V3, Q52KU6, Q5EB32, Q5F452, Q5R6F6, Q5R9S3, Q5U581, Q62688, Q6AXQ4, Q6NU08, Q6TEL0, Q6XPS3, Q7TPM9, Q7ZXF1, Q8K394, Q8NCE2, Q8VE11, Q8VEL2, Q96EF0, Q96MI9

Diamond homologs: A0A0G2JXT6, A0JMK5, A2BGG1, A4FU01, A6QLT2, A6QLT4, A7MB43, E9PXF8, F4J3T8, F4JWB3, G5ED68, O13819, P47147, Q13496, Q13613, Q13614, Q13615, Q22712, Q2KJ24, Q3V1L6, Q52KU6, Q54GQ1, Q55E58, Q5EB32, Q5F452, Q5PQT2, Q5R6F6, Q5R9S3, Q5REB9, Q5U581, Q5ZIV1, Q6AXQ4, Q6NTN5, Q6NU08, Q6TEL0, Q7TPM9, Q7ZXF1, Q80TA6, Q8K296, Q8VE11

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 76 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
Constitutive Signaling by Aberrant PI3K in Cancer	5	13.2×	2e-03
PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling	6	12.1×	2e-03
PIP3 activates AKT signaling	8	11.1×	2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	282
Likely benign	18
Benign	6

Top pathogenic / likely-pathogenic (0)

SpliceAI

4445 predictions. Top by Δscore:

Variant	Effect	Δscore
8:11285067:AGCGG:A	donor_loss	1.0000
8:11285068:GCG:G	donor_gain	1.0000
8:11285068:GCGGT:G	donor_loss	1.0000
8:11285069:CGG:C	donor_loss	1.0000
8:11285071:G:C	donor_loss	1.0000
8:11285071:G:GG	donor_gain	1.0000
8:11285072:TGAG:T	donor_loss	1.0000
8:11292333:G:A	acceptor_gain	1.0000
8:11295192:A:AG	acceptor_gain	1.0000
8:11295192:A:C	acceptor_loss	1.0000
8:11295193:G:GA	acceptor_gain	1.0000
8:11295193:GA:G	acceptor_gain	1.0000
8:11295193:GAT:G	acceptor_gain	1.0000
8:11295193:GATTT:G	acceptor_gain	1.0000
8:11295298:TTGAG:T	donor_gain	1.0000
8:11295299:TGAGG:T	donor_loss	1.0000
8:11295300:GAG:G	donor_gain	1.0000
8:11295301:AGGTA:A	donor_loss	1.0000
8:11295303:G:GG	donor_gain	1.0000
8:11295303:GTA:G	donor_loss	1.0000
8:11300146:GCT:G	donor_gain	1.0000
8:11304840:GACCA:G	acceptor_gain	1.0000
8:11305010:GGATG:G	donor_gain	1.0000
8:11305011:GATG:G	donor_gain	1.0000
8:11305011:GATGG:G	donor_gain	1.0000
8:11305013:TGG:T	donor_loss	1.0000
8:11305014:GGTA:G	donor_loss	1.0000
8:11305015:GTAA:G	donor_loss	1.0000
8:11305016:TAAG:T	donor_loss	1.0000
8:11306344:G:GT	donor_gain	1.0000

AlphaMissense

3625 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:11284967:G:C	G27R	0.999
8:11284974:T:C	L29P	0.999
8:11284998:T:A	I37N	0.999
8:11284998:T:C	I37T	0.999
8:11285037:T:C	L50P	0.999
8:11295232:A:T	K74I	0.999
8:11306379:T:A	W261R	0.999
8:11306379:T:C	W261R	0.999
8:11315056:T:A	W369R	0.999
8:11315056:T:C	W369R	0.999
8:11316790:T:C	F411L	0.999
8:11316792:T:A	F411L	0.999
8:11316792:T:G	F411L	0.999
8:11319803:C:A	P484H	0.999
8:11284908:T:A	I7N	0.998
8:11284968:G:A	G27D	0.998
8:11284976:T:C	C30R	0.998
8:11284988:C:G	H34D	0.998
8:11284991:C:G	H35D	0.998
8:11284998:T:G	I37S	0.998
8:11285033:T:A	W49R	0.998
8:11285033:T:C	W49R	0.998
8:11295233:A:C	K74N	0.998
8:11295233:A:T	K74N	0.998
8:11295294:T:C	S95P	0.998
8:11295295:C:T	S95F	0.998
8:11300065:T:C	F112L	0.998
8:11300067:T:A	F112L	0.998
8:11300067:T:G	F112L	0.998
8:11309627:T:A	W304R	0.998

dbSNP variants (sampled 300 via entrez): RS1000057844 (8:11308646 C>T), RS1000070622 (8:11312864 C>A,T), RS1000077194 (8:11306582 C>G,T), RS1000106219 (8:11290373 T>A,C), RS1000163948 (8:11293513 T>C), RS1000186184 (8:11289319 G>A,C), RS1000210991 (8:11293803 G>T), RS1000358180 (8:11312614 G>C,T), RS1000485165 (8:11323138 A>G), RS1000520417 (8:11296807 G>A,C), RS1000534497 (8:11306747 A>G), RS1000536892 (8:11314568 A>C), RS1000589588 (8:11309847 T>C), RS1000612871 (8:11318313 G>A), RS1000642052 (8:11310050 A>G)

Disease associations

OMIM: gene MIM:606260 | disease phenotypes: MIM:148840

GenCC curated gene-disease

Mondo (1): Kleine-Levin syndrome (MONDO:0007863)

Orphanet (1): Kleine-Levin syndrome (Orphanet:33543)

HPO phenotypes

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

GWAS associations

27 associations (top):

Study	Trait	p-value
GCST000847_5	Retinal vascular caliber	4.000000e-07
GCST003103_2	Systemic lupus erythematosus	8.000000e-06
GCST004015_2	Extraversion	2.000000e-09
GCST004351_19	Bone ultrasound measurement (broadband ultrasound attenuation)	4.000000e-07
GCST007324_147	Adventurousness	5.000000e-10
GCST007324_35	Adventurousness	3.000000e-08
GCST007709_219	General factor of neuroticism	1.000000e-08
GCST010002_269	Refractive error	1.000000e-24
GCST010132_11	Processed meat consumption	4.000000e-10
GCST010132_14	Processed meat consumption	2.000000e-15
GCST010132_15	Processed meat consumption	1.000000e-09
GCST010136_40	Fruit consumption	1.000000e-10
GCST010136_5	Fruit consumption	9.000000e-09
GCST010136_9	Fruit consumption	1.000000e-08
GCST010142_4	Fish- and plant-related diet	2.000000e-12
GCST010142_6	Fish- and plant-related diet	3.000000e-12
GCST010142_63	Fish- and plant-related diet	2.000000e-12
GCST010142_67	Fish- and plant-related diet	1.000000e-10
GCST010142_70	Fish- and plant-related diet	8.000000e-10
GCST010142_89	Fish- and plant-related diet	4.000000e-16
GCST010142_90	Fish- and plant-related diet	7.000000e-15
GCST010703_306	Brain morphology (MOSTest)	5.000000e-26
GCST010774_7	Essential hypertension (time to event)	1.000000e-07
GCST012226_771	Waist circumference adjusted for body mass index	4.000000e-10
GCST012228_570	Waist-hip index	3.000000e-10
GCST012230_570	Waist-to-hip ratio adjusted for BMI	2.000000e-10
GCST012230_76	Waist-to-hip ratio adjusted for BMI	2.000000e-09

EFO canonical traits (10, from GWAS)

EFO ID	Trait name
EFO:0004731	eye measurement
EFO:0004317	extraversion
EFO:0004514	bone quantitative ultrasound measurement
EFO:0008579	risk-taking behaviour
EFO:0007660	neuroticism measurement
EFO:0008111	diet measurement
EFO:0004346	neuroimaging measurement
EFO:0004918	age at diagnosis
EFO:0007789	BMI-adjusted waist circumference
EFO:0007788	BMI-adjusted waist-hip ratio

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D017593	Kleine-Levin Syndrome	C10.886.425.800.200.500; F03.870.400.800.200.500

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Acetaminophen	increases expression, affects response to substance	3
Air Pollutants	increases expression, decreases expression, increases abundance	2
Benzo(a)pyrene	affects methylation, increases expression	2
Smoke	decreases expression, increases abundance, increases expression	2
triphenyl phosphate	affects expression	1
arsenite	decreases reaction, affects binding	1
sodium arsenite	increases expression	1
coumarin	decreases phosphorylation	1
ICG 001	increases expression	1
abrine	increases expression	1
Arsenic	affects methylation	1
Atrazine	decreases expression	1
Coal	decreases expression, increases abundance	1
Ivermectin	decreases expression	1
Quercetin	decreases phosphorylation	1
Selenium	decreases expression	1
Dihydrotestosterone	increases expression	1
Tretinoin	increases expression	1
Urethane	increases expression	1
Valproic Acid	decreases expression	1
Vitamin E	decreases expression	1
Cadmium Chloride	increases expression	1
Okadaic Acid	increases expression	1
Copper Sulfate	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT01793168	Not specified	RECRUITING	Rare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
NCT02337023	Not specified	COMPLETED	Brain Scintigraphy in Normal Versus Kleine-Levin Syndrome Subjects
NCT03754348	Not specified	COMPLETED	Microglial Activation in Narcolepsy Type 1 and Kleine-Levin Syndrome: Positron Emission Tomography (PET) Study in [18F] DPA-714