STX6

Summary

STX6 (syntaxin 6, HGNC:11441) is a protein-coding gene on chromosome 1q25.3, encoding Syntaxin-6 (O43752). SNARE promoting movement of transport vesicles to target membranes.

Enables syntaxin binding activity. Involved in regulation of protein localization; retrograde transport, endosome to Golgi; and vesicle fusion. Acts upstream of or within endocytic recycling. Located in several cellular components, including early endosome; perinuclear region of cytoplasm; and trans-Golgi network. Part of SNARE complex.

Source: NCBI Gene 10228 — RefSeq curated summary.

At a glance

• GWAS associations: 12
• Clinical variants (ClinVar): 53 total
• MANE Select transcript: NM_005819

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11441
Approved symbol	STX6
Name	syntaxin 6
Location	1q25.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000135823
Ensembl biotype	protein_coding
OMIM	603944
Entrez	10228

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000258301, ENST00000469135, ENST00000496476, ENST00000542060

RefSeq mRNA: 2 — MANE Select: NM_005819 NM_001286210, NM_005819

CCDS: CCDS1341, CCDS65738

Canonical transcript exons

ENST00000258301 — 8 exons

Exon	Start	End
ENSE00000822708	180988239	180988345
ENSE00000822709	180989984	180990109
ENSE00001434793	181005294	181005463
ENSE00001434832	181002606	181002700
ENSE00001445082	181022639	181022870
ENSE00001955708	180972725	180976646
ENSE00003513011	180993363	180993425
ENSE00003649817	180984677	180984771

Expression profiles

Bgee: expression breadth ubiquitous, 278 present calls, max score 98.76.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.2805 / max 392.7626, expressed in 1815 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
16109	21.2805	1815

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	98.76	gold quality
oocyte	CL:0000023	96.22	gold quality
cortical plate	UBERON:0005343	93.15	gold quality
endothelial cell	CL:0000115	92.94	gold quality
esophagus squamous epithelium	UBERON:0006920	91.98	gold quality
gingival epithelium	UBERON:0001949	91.57	gold quality
gingiva	UBERON:0001828	91.42	gold quality
ganglionic eminence	UBERON:0004023	91.10	gold quality
epithelium of esophagus	UBERON:0001976	89.72	gold quality
Brodmann (1909) area 23	UBERON:0013554	89.45	gold quality
upper leg skin	UBERON:0004262	88.87	gold quality
skin of hip	UBERON:0001554	88.86	gold quality
monocyte	CL:0000576	88.64	gold quality
primary visual cortex	UBERON:0002436	88.56	gold quality
cartilage tissue	UBERON:0002418	88.31	gold quality
mononuclear cell	CL:0000842	88.05	gold quality
squamous epithelium	UBERON:0006914	87.99	gold quality
middle temporal gyrus	UBERON:0002771	87.96	gold quality
leukocyte	CL:0000738	87.91	gold quality
lower esophagus mucosa	UBERON:0035834	87.68	gold quality
epithelium of nasopharynx	UBERON:0001951	87.21	gold quality
esophagus mucosa	UBERON:0002469	86.94	gold quality
prefrontal cortex	UBERON:0000451	86.83	gold quality
cerebellar hemisphere	UBERON:0002245	86.71	gold quality
cerebellar cortex	UBERON:0002129	86.69	gold quality
postcentral gyrus	UBERON:0002581	86.50	gold quality
superior frontal gyrus	UBERON:0002661	86.39	gold quality
cerebellum	UBERON:0002037	86.28	gold quality
ventricular zone	UBERON:0003053	86.28	gold quality
blood	UBERON:0000178	86.27	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.70

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

153 targeting STX6, 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-3613-3P	100.00	76.36	7965
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-9-3P	99.96	70.88	2068
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-130A-3P	99.90	73.31	1861

Literature-anchored findings (GeneRIF, showing 24)

• STX6 can be induced by DNA damage and Mdm2 inhibitor Nutlin-3 in a p53-dependent manner. (PMID:18779328)
• Syntaxin 6 and CAL mediate the degradation of the cystic fibrosis transmembrane conductance regulator (PMID:20130090)
• Importance of syntaxin 6 in the maintenance of cellular VEGFR2 levels.The inhibitory form of syntaxin 6 has good potential as an antiangiogenic agent. (PMID:21063020)
• The trans-Golgi SNARE protein syntaxin 6 is recruited to the chlamydial inclusion in a manner that requires chlamydial protein synthesis and is conserved among all chlamydial species examined. (PMID:21109560)
• COG directly and positively regulates endosome-to-TGN retrograde transport by specific and direct interaction with the t-SNARE Stx6 via its Cog6 subunit. (PMID:21807881)
• syntaxin 6-regulated membrane trafficking events control outside-in signaling via haptotactic and chemotactic mechanisms. (PMID:21880737)
• A review of the various roles of the Golgi- and endosome-localized t-SNARE, syntaxin-6, in membrane trafficking during physiological as well as pathological conditions. [Review] (PMID:22489884)
• Data suggest a new integrin trafficking pathway in which endocytosed integrins are transported from VAMP3-containing recycling endosomes to STX6-containing trans-Golgi network before being recycled to the plasma membrane. (PMID:22573826)
• No pathogenic mutations are found in syntaxin 6 that are associated with risk of Parkinson’s disease. (PMID:23415606)
• colocalization of ATP11B with fluorescent cisplatin and with vesicular trafficking proteins, such as STX6 and VAMP4, strongly suggests that ATP11B contributes to secretory vesicular transport of cisplatin from Golgi to plasma membrane (PMID:23585472)
• Data indicate that depletion of VAMP4, syntaxin 6, syntaxin 16, and Vti1a disrupted the Golgi ribbon structure. (PMID:23677696)
• Syntaxin 6 and VAMP4 colocalize to the chlamydial inclusion. (PMID:23798538)
• Data indicate that E3 ubiquitin ligase MARCH2 co-immunoprecipitated and co-localized with CAL and syntaxin 6 (STX6), and show the ubiquitination of CFTR by MARCH2. (PMID:23818989)
• A dityrosine motif of Ang2 interacts with a highly conserved groove in Syntaxin 6. (PMID:23932592)
• The compartment-specific interaction of Syntaxin 6 with v-SNARES VAMP3 and VAMP4 are controlled through an ability of Syntaxin 6 to sense cholesterol levels in the trans-Golgi network and recycling endosomes. (PMID:24746815)
• the expression of STX6 was up-regulated in esophageal squamous cell carcinoma samples, and its expression was significantly correlated with tumor size, histological differentiation, lymph node metastasis and depth (PMID:26906622)
• RABGEF1 mediates recycling endosome fusion with GAS-containing autophagosome-like vacuoles through the STX6-VAMP3-VTI1B complex; SNAREs are involved in autophagosome formation in response to bacterial infection (PMID:27791468)
• Potent inhibition of human cytomegalovirus has been reported by modulation of host cellular STX6. (PMID:27795424)
• Syntaxin 6: A novel predictive and prognostic biomarker in papillary renal cell carcinoma. (PMID:30816681)
• Human Cytomegalovirus Manipulates Syntaxin 6 for Successful Trafficking and Subsequent Infection of Monocytes. (PMID:35862696)
• Syntaxin 6 Enhances the Progression of Epithelial Ovarian Cancer by Promoting Cancer Cell Proliferation. (PMID:37378930)
• Syntaxin-6 promotes the progression of hepatocellular carcinoma and alters its sensitivity to chemotherapies by activating the USF2/LC3B axis. (PMID:37564208)
• N[6] -methyladenosine-modified circSTX6 promotes hepatocellular carcinoma progression by regulating the HNRNPD/ATF3 axis and encoding a 144 amino acid polypeptide. (PMID:37877357)
• Intracellular trafficking of HIV-1 Gag via Syntaxin 6-positive compartments/vesicles: Involvement in tumor necrosis factor secretion. (PMID:38280430)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	stx6	ENSDARG00000042742
mus_musculus	Stx6	ENSMUSG00000026470
rattus_norvegicus	Stx6	ENSRNOG00000003402
drosophila_melanogaster	Syx6	FBGN0037084
caenorhabditis_elegans		WBGENE00015789

Paralogs (2): STX10 (ENSG00000104915), STX8 (ENSG00000170310)

Protein

Protein identifiers

Syntaxin-6 — O43752 (reviewed: O43752)

All UniProt accessions (1): O43752

UniProt curated annotations — full annotation on UniProt →

Function. SNARE promoting movement of transport vesicles to target membranes. Targets endosomes to the trans-Golgi network, and may therefore function in retrograde trafficking. Together with SNARE STX12, promotes movement of vesicles from endosomes to the cell membrane, and may therefore function in the endocytic recycling pathway.

Subunit / interactions. Identified in a complex containing STX6, STX12, VAMP4 and VTI1A. Binds EEA1. Interacts with VPS45A. Interacts with MARCHF2; the interaction promotes MARCHF2-mediated ubiquitination and degradation of CFTR. Interacts with MARCHF3. Interacts with GOPC. Interacts with BLTP3B (via C-terminal coiled-coil domain). Interacts with BAIAP3; this interaction is increased in the presence of calcium. Interacts with VPS13B.

Subcellular location. Golgi apparatus membrane. Golgi apparatus. trans-Golgi network membrane. Recycling endosome membrane.

Similarity. Belongs to the syntaxin family.

Isoforms (2)

UniProt ID	Names	Canonical?
O43752-1	1	yes
O43752-2	2

RefSeq proteins (2): NP_001273139, NP_005810* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000727	T_SNARE_dom	Domain
IPR006012	Syntaxin/epimorphin_CS	Conserved_site
IPR010989	SNARE	Homologous_superfamily
IPR015260	Syntaxin-6/10/61_N	Domain

Pfam: PF05739, PF09177

UniProt features (19 total): helix 5, modified residue 4, initiator methionine 1, chain 1, splice variant 1, sequence conflict 1, turn 1, topological domain 1, transmembrane region 1, domain 1, region of interest 1, coiled-coil region 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
4J2C	X-RAY DIFFRACTION	1.8
2NPS	X-RAY DIFFRACTION	2.5

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O43752-F1	82.11	0.37

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 (4): 152, 2, 2, 129

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

ID	Pathway
R-HSA-6811438	Intra-Golgi traffic
R-HSA-6811440	Retrograde transport at the Trans-Golgi-Network
R-HSA-199991	Membrane Trafficking
R-HSA-5653656	Vesicle-mediated transport
R-HSA-6811442	Intra-Golgi and retrograde Golgi-to-ER traffic

MSigDB gene sets: 306 (showing top): MULLIGHAN_NPM1_SIGNATURE_3_UP, GOBP_ENDOSOME_ORGANIZATION, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, TGCACTT_MIR519C_MIR519B_MIR519A, GOBP_VESICLE_ORGANIZATION, AAGCCAT_MIR135A_MIR135B, MAZ_Q6, GOBP_MEMBRANE_FUSION, GOBP_VESICLE_MEDIATED_TRANSPORT, ATGCAGT_MIR217, REACTOME_MEMBRANE_TRAFFICKING, GOBP_MEMBRANE_DOCKING, GOCC_TRANS_GOLGI_NETWORK, FOSTER_TOLERANT_MACROPHAGE_UP, GOBP_ORGANELLE_MEMBRANE_FUSION

GO Biological Process (11): intracellular protein transport (GO:0006886), vesicle fusion (GO:0006906), synaptic vesicle to endosome fusion (GO:0016189), endocytic recycling (GO:0032456), regulation of protein localization (GO:0032880), retrograde transport, endosome to Golgi (GO:0042147), Golgi vesicle transport (GO:0048193), obsolete vesicle docking (GO:0048278), endosome organization (GO:0007032), protein transport (GO:0015031), vesicle-mediated transport (GO:0016192)

GO Molecular Function (4): SNARE binding (GO:0000149), SNAP receptor activity (GO:0005484), syntaxin binding (GO:0019905), protein binding (GO:0005515)

GO Cellular Component (20): Golgi membrane (GO:0000139), nucleoplasm (GO:0005654), early endosome (GO:0005769), Golgi apparatus (GO:0005794), trans-Golgi network (GO:0005802), cytosol (GO:0005829), plasma membrane (GO:0005886), endomembrane system (GO:0012505), clathrin-coated vesicle (GO:0030136), synaptic vesicle membrane (GO:0030672), SNARE complex (GO:0031201), trans-Golgi network membrane (GO:0032588), phagocytic vesicle (GO:0045335), perinuclear region of cytoplasm (GO:0048471), recycling endosome (GO:0055037), recycling endosome membrane (GO:0055038), endosome (GO:0005768), membrane (GO:0016020), organelle membrane (GO:0031090), vesicle (GO:0031982)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Intra-Golgi and retrograde Golgi-to-ER traffic	2
Vesicle-mediated transport	1
Membrane Trafficking	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
cytoplasm	4
intracellular protein localization	3
vesicle organization	2
vesicle-mediated transport	2
endosomal transport	2
transport	2
endosome	2
endomembrane system	2
membrane	2
membrane-bounded organelle	2
protein transport	1
intracellular transport	1
organelle membrane fusion	1
endosome organization	1
organelle fusion	1
synaptic vesicle endosomal processing	1
vesicle-mediated transport to the plasma membrane	1
regulation of localization	1
intercellular transport	1
cytosolic transport	1
endomembrane system organization	1
establishment of protein localization	1
cellular process	1
protein binding	1
protein-macromolecule adaptor activity	1
membrane fusion	1
fusogenic activity	1
SNARE binding	1
binding	1
Golgi apparatus	1
bounding membrane of organelle	1
nuclear lumen	1
intracellular membrane-bounded organelle	1
Golgi apparatus subcompartment	1
cell periphery	1
vacuole	1
plasma membrane	1
coated vesicle	1
synaptic vesicle	1

Protein interactions and networks

STRING

2000 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
STX6	VAMP4	O75379	999
STX6	VAMP3	Q15836	996
STX6	STX16	O14662	996
STX6	VTI1A	Q96AJ9	995
STX6	VTI1B	Q9UEU0	985
STX6	GOPC	Q9HD26	967
STX6	EEA1	Q15075	960
STX6	VAMP2	P19065	953
STX6	SNAP23	O00161	951
STX6	STX7	O15400	949
STX6	VAMP7	P51809	943
STX6	VAMP8	Q9BV40	941
STX6	MARCHF2	Q9P0N8	932
STX6	STX4	Q12846	913
STX6	STX3	Q13277	909

IntAct

227 interactions, top by confidence:

A	B	Type	Score
STX4	STX6	psi-mi:“MI:0915”(physical association)	0.870
STX6	STX4	psi-mi:“MI:0915”(physical association)	0.870
STX18	NBAS	psi-mi:“MI:0914”(association)	0.810
NAPA	SNAP23	psi-mi:“MI:0914”(association)	0.780
STX6	NAPB	psi-mi:“MI:0915”(physical association)	0.740
NAPB	STX6	psi-mi:“MI:0915”(physical association)	0.740
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
STX6	SNAP29	psi-mi:“MI:0915”(physical association)	0.690
GOSR2	STX6	psi-mi:“MI:0915”(physical association)	0.670
STX6	GOSR2	psi-mi:“MI:0915”(physical association)	0.670
VAMP4	STX6	psi-mi:“MI:0915”(physical association)	0.670
STX6	TMEM9	psi-mi:“MI:0915”(physical association)	0.670
FAM9C	NDC80	psi-mi:“MI:0914”(association)	0.670
STX6	GOSR2	psi-mi:“MI:0914”(association)	0.670
VPS51	STX6	psi-mi:“MI:0407”(direct interaction)	0.660
VPS51	STX6	psi-mi:“MI:0915”(physical association)	0.660
VPS51	STX6	psi-mi:“MI:0914”(association)	0.660

BioGRID (625): STX6 (Two-hybrid), STX6 (Two-hybrid), STX6 (Two-hybrid), NAPB (Two-hybrid), STX6 (Affinity Capture-RNA), STX6 (Affinity Capture-RNA), STX6 (Affinity Capture-RNA), STX6 (Affinity Capture-Western), STX6 (Affinity Capture-Western), STX6 (Affinity Capture-Western), STX6 (Affinity Capture-Western), STX6 (Affinity Capture-MS), VPS45 (Affinity Capture-MS), NAPA (Affinity Capture-MS), STX4 (Affinity Capture-MS)

ESM2 similar proteins: A4FUD6, B5KFI0, D3ZKU7, O43752, O55102, O75486, P60228, P60229, P78537, Q05AY2, Q05B58, Q08DP2, Q08DU8, Q0VFD8, Q1LUA8, Q2NKW0, Q32L03, Q32WR5, Q3B8M3, Q3SZ60, Q3T102, Q4R6G8, Q4R7C8, Q5R6Q2, Q5R7L8, Q5R8K9, Q5R8N4, Q5ZJA9, Q5ZL19, Q5ZLA5, Q63635, Q641X8, Q66KB9, Q6I9Y2, Q6P643, Q6P7L9, Q6QNY1, Q7SZ78, Q7TMY4, Q7Z3J2

Diamond homologs: O43752, O60499, P83528, Q5R6Q2, Q5ZL19, Q63635, Q9JKK1, O88983, Q3T075, Q54IX6, Q946Y7, Q9HGN3, Q9UNK0, Q9Z2Q7, Q553P5, Q9SA23

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 130 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
Intra-Golgi traffic	11	37.6×	2e-12
Retrograde transport at the Trans-Golgi-Network	11	31.8×	6e-12
trans-Golgi Network Vesicle Budding	7	23.4×	2e-06
COPII-mediated vesicle transport	7	15.0×	2e-05
RHOJ GTPase cycle	5	13.2×	5e-04
Intra-Golgi and retrograde Golgi-to-ER traffic	9	12.4×	3e-06
RHOQ GTPase cycle	5	11.9×	7e-04
COPI-mediated anterograde transport	8	11.6×	2e-05

GO biological processes:

GO term	Partners	Fold	FDR
obsolete vesicle docking	9	61.0×	3e-12
vesicle fusion	10	53.3×	1e-12
post-Golgi vesicle-mediated transport	5	46.6×	4e-06
membrane fusion	7	38.7×	5e-08
intra-Golgi vesicle-mediated transport	8	37.3×	4e-09
exocytosis	14	18.8×	5e-12
endocytic recycling	6	14.2×	2e-04
retrograde transport, endosome to Golgi	6	10.9×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	38
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1922 predictions. Top by Δscore:

Variant	Effect	Δscore
1:180984676:CCA:C	donor_gain	1.0000
1:180984767:ACATA:A	acceptor_gain	1.0000
1:180984768:CATA:C	acceptor_gain	1.0000
1:180984768:CATAC:C	acceptor_gain	1.0000
1:180984769:ATA:A	acceptor_gain	1.0000
1:180984769:ATAC:A	acceptor_loss	1.0000
1:180984770:TA:T	acceptor_gain	1.0000
1:180984770:TACTA:T	acceptor_loss	1.0000
1:180984771:AC:A	acceptor_loss	1.0000
1:180984772:C:CC	acceptor_gain	1.0000
1:180984772:CTAG:C	acceptor_loss	1.0000
1:180988231:ATACT:A	donor_loss	1.0000
1:180988233:ACTC:A	donor_loss	1.0000
1:180988236:CACA:C	donor_loss	1.0000
1:180988237:A:AC	donor_gain	1.0000
1:180988237:A:AG	donor_loss	1.0000
1:180988238:C:CA	donor_gain	1.0000
1:180988238:CA:C	donor_gain	1.0000
1:180988238:CACT:C	donor_gain	1.0000
1:180988238:CACTG:C	donor_gain	1.0000
1:180988341:ATCAA:A	acceptor_gain	1.0000
1:180988342:TCAA:T	acceptor_gain	1.0000
1:180988343:CAA:C	acceptor_gain	1.0000
1:180988343:CAAC:C	acceptor_gain	1.0000
1:180988344:AA:A	acceptor_gain	1.0000
1:180988346:C:CC	acceptor_gain	1.0000
1:180988346:C:CG	acceptor_loss	1.0000
1:180988347:T:C	acceptor_loss	1.0000
1:180988349:G:C	acceptor_gain	1.0000
1:180988349:G:GC	acceptor_gain	1.0000

AlphaMissense

1693 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:181002642:T:A	R88S	1.000
1:181002642:T:G	R88S	1.000
1:181002672:A:C	F78L	1.000
1:181002672:A:T	F78L	1.000
1:181002674:A:G	F78L	1.000
1:181005308:A:G	L64P	1.000
1:181005317:A:G	L61P	1.000
1:181005324:A:G	W59R	1.000
1:181005324:A:T	W59R	1.000
1:181005338:A:G	L54P	1.000
1:181005350:A:G	L50P	1.000
1:180988254:A:G	L194P	0.999
1:180988276:A:G	S187P	0.999
1:180988287:A:G	L183P	0.999
1:181002633:G:C	F91L	0.999
1:181002633:G:T	F91L	0.999
1:181002635:A:G	F91L	0.999
1:181002643:C:A	R88I	0.999
1:181002643:C:G	R88T	0.999
1:181002673:A:G	F78S	0.999
1:181002694:A:T	V71D	0.999
1:181005308:A:T	L64H	0.999
1:181005311:T:C	D63G	0.999
1:181005311:T:G	D63A	0.999
1:181005312:C:G	D63H	0.999
1:181005322:C:A	W59C	0.999
1:181005322:C:G	W59C	0.999
1:181005329:A:T	I57K	0.999
1:181005335:C:G	R55P	0.999
1:181005450:C:G	A17P	0.999

dbSNP variants (sampled 300 via entrez): RS1000038024 (1:181009882 C>G), RS1000088599 (1:181010077 G>A,C), RS1000145183 (1:180977614 T>C), RS1000189084 (1:181016007 T>C), RS1000193783 (1:181010633 CTTT>C,CT,CTT,CTTTT), RS1000258679 (1:180973857 C>T), RS1000288159 (1:180974129 G>A,C), RS1000323562 (1:180986146 C>T), RS1000359444 (1:181004379 C>T), RS1000368729 (1:181022692 G>A,C,T), RS1000369116 (1:180981019 G>A), RS1000457000 (1:181022536 G>A,C), RS1000481514 (1:180980161 C>T), RS1000543876 (1:180998430 TG>T), RS1000595642 (1:181014158 G>A)

Disease associations

OMIM: gene MIM:603944 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

12 associations (top):

Study	Trait	p-value
GCST001116_1	Progressive supranuclear palsy	4.000000e-11
GCST005312_29	Menopause (age at onset)	1.000000e-10
GCST006418_7	Progressive supranuclear palsy	9.000000e-16
GCST010697_5	Cortical surface area (min-P)	4.000000e-11
GCST010698_73	Subcortical volume (min-P)	1.000000e-13
GCST010699_38	Brain morphology (min-P)	1.000000e-08
GCST010700_67	Cortical thickness (MOSTest)	4.000000e-09
GCST010701_105	Cortical surface area (MOSTest)	3.000000e-12
GCST010702_28	Subcortical volume (MOSTest)	6.000000e-11
GCST010703_252	Brain morphology (MOSTest)	4.000000e-14
GCST012006_1	Intralaminar thalamic nuclei volume	5.000000e-12
GCST90001389_2	Creutzfeldt-Jakob disease (sporadic)	1.000000e-10

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004704	age at menopause
EFO:0004346	neuroimaging measurement
EFO:0004840	cortical thickness
EFO:0006935	thalamus volume
EFO:1000656	sporadic Creutzfeld Jacob disease

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases methylation, increases expression	4
Aflatoxin B1	affects expression, increases expression, increases methylation	3
Benzo(a)pyrene	affects methylation, increases expression	2
Formaldehyde	increases expression	2
Cadmium Chloride	decreases expression, increases abundance, increases expression	2
FR900359	affects phosphorylation	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, increases expression	1
kojic acid	increases expression	1
beta-lapachone	increases expression	1
sodium arsenite	affects cotreatment, increases expression	1
cobaltous chloride	increases expression	1
coumarin	increases phosphorylation	1
vanadyl sulfate	increases expression	1
pinosylvin	increases expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	affects binding, increases reaction	1
corosolic acid	increases expression	1
Acetaminophen	increases expression	1
Cadmium	increases abundance, increases expression	1
Caffeine	decreases phosphorylation	1
Cisplatin	increases expression	1
Demecolcine	increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Ethyl Methanesulfonate	increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Rotenone	decreases expression	1
Tobacco Smoke Pollution	increases expression	1

Clinical trials (associated diseases)

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