VAMP4

Summary

VAMP4 (vesicle associated membrane protein 4, HGNC:12645) is a protein-coding gene on chromosome 1q24.3, encoding Vesicle-associated membrane protein 4 (O75379). Involved in the pathway that functions to remove an inhibitor (probably synaptotagmin-4) of calcium-triggered exocytosis during the maturation of secretory granules.

Synaptobrevins/VAMPs, syntaxins, and the 25-kD synaptosomal-associated protein SNAP25 are the main components of a protein complex involved in the docking and/or fusion of synaptic vesicles with the presynaptic membrane. The protein encoded by this gene is a member of the vesicle-associated membrane protein (VAMP)/synaptobrevin family. This protein may play a role in trans-Golgi network-to-endosome transport.

Source: NCBI Gene 8674 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 39 total
• MANE Select transcript: NM_003762

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12645
Approved symbol	VAMP4
Name	vesicle associated membrane protein 4
Location	1q24.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000117533
Ensembl biotype	protein_coding
OMIM	606909
Entrez	8674

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 7 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000236192, ENST00000367740, ENST00000474047, ENST00000482519, ENST00000926427, ENST00000926428, ENST00000969944, ENST00000969945, ENST00000969946

RefSeq mRNA: 2 — MANE Select: NM_003762 NM_001185127, NM_003762

CCDS: CCDS1298, CCDS53430

Canonical transcript exons

ENST00000236192 — 8 exons

Exon	Start	End
ENSE00000789793	171710714	171710814
ENSE00001701696	171700160	171704534
ENSE00001873338	171741910	171742065
ENSE00003574399	171709665	171709744
ENSE00003625814	171719171	171719221
ENSE00003635815	171706367	171706418
ENSE00003665990	171728524	171728570
ENSE00003679236	171738349	171738463

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 97.45.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.4306 / max 192.2759, expressed in 1817 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
15900	16.7700	1815
15899	0.9150	558
15898	0.7767	476
15897	0.6939	396
15902	0.1504	45
15901	0.1245	49

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	97.45	gold quality
Brodmann (1909) area 23	UBERON:0013554	97.30	gold quality
middle temporal gyrus	UBERON:0002771	96.91	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	96.52	gold quality
inferior olivary complex	UBERON:0002127	95.33	gold quality
blood vessel layer	UBERON:0004797	95.14	gold quality
pons	UBERON:0000988	94.87	gold quality
substantia nigra pars compacta	UBERON:0001965	94.57	gold quality
lateral nuclear group of thalamus	UBERON:0002736	94.38	gold quality
cerebellar vermis	UBERON:0004720	94.33	gold quality
tibia	UBERON:0000979	94.19	gold quality
medulla oblongata	UBERON:0001896	94.09	gold quality
superior vestibular nucleus	UBERON:0007227	93.93	gold quality
cervix squamous epithelium	UBERON:0006922	93.54	gold quality
substantia nigra pars reticulata	UBERON:0001966	93.47	gold quality
CA1 field of hippocampus	UBERON:0003881	93.30	gold quality
visceral pleura	UBERON:0002401	93.13	gold quality
ventral tegmental area	UBERON:0002691	93.08	gold quality
entorhinal cortex	UBERON:0002728	92.98	gold quality
gingival epithelium	UBERON:0001949	92.87	gold quality
parotid gland	UBERON:0001831	92.86	gold quality
lateral globus pallidus	UBERON:0002476	92.80	gold quality
parietal lobe	UBERON:0001872	92.47	gold quality
postcentral gyrus	UBERON:0002581	92.44	gold quality
superior frontal gyrus	UBERON:0002661	92.08	gold quality
choroid plexus epithelium	UBERON:0003911	92.08	gold quality
cranial nerve II	UBERON:0000941	91.99	gold quality
pleura	UBERON:0000977	91.73	gold quality
parietal pleura	UBERON:0002400	91.67	gold quality
dorsal root ganglion	UBERON:0000044	91.65	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.86

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NR1I2

miRNA regulators (miRDB)

165 targeting VAMP4, 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-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-6867-5P	100.00	82.21	3464
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-3688-3P	99.97	72.02	2834

Literature-anchored findings (GeneRIF, showing 8)

• VAMP7 is involved in many fusion processes and thus plays a more general function in NK-cell activity than VAMP4. (PMID:21805468)
• The findings of this study suggested that VAMP4 and syb2 diverge functionally, traffic independently and support distinct forms of neurotransmission (PMID:22406549)
• 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)
• CALM is able to sort VAMP4 and VAMP7, even though they have sorting signals for other clathrin adaptors. (PMID:23741335)
• Syntaxin 6 and VAMP4 colocalize to the chlamydial inclusion. (PMID:23798538)
• Analysis of DNM3 and VAMP4 as genetic modifiers of LRRK2 Parkinson’s disease. (PMID:32873436)
• VAMP4 regulates insulin levels by targeting secretory granules to lysosomes. (PMID:36053215)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	vamp4	ENSDARG00000043510
mus_musculus	Vamp4	ENSMUSG00000026696
rattus_norvegicus	Vamp4	ENSRNOG00000003071
caenorhabditis_elegans		WBGENE00004899
caenorhabditis_elegans		WBGENE00014084
caenorhabditis_elegans		WBGENE00044062

Paralogs (10): VAMP3 (ENSG00000049245), SEC22C (ENSG00000093183), YKT6 (ENSG00000106636), VAMP8 (ENSG00000118640), SEC22A (ENSG00000121542), VAMP7 (ENSG00000124333), VAMP1 (ENSG00000139190), VAMP5 (ENSG00000168899), VAMP2 (ENSG00000220205), SEC22B (ENSG00000265808)

Protein

Protein identifiers

Vesicle-associated membrane protein 4 — O75379 (reviewed: O75379)

All UniProt accessions (2): O75379, Q6IAZ3

UniProt curated annotations — full annotation on UniProt →

Function. Involved in the pathway that functions to remove an inhibitor (probably synaptotagmin-4) of calcium-triggered exocytosis during the maturation of secretory granules. May be a marker for this sorting pathway that is critical for remodeling the secretory response of granule.

Subunit / interactions. Identified in a complex containing STX6, STX12, VAMP4 and VTI1A. Interacts with BAIAP3; this interaction is increased in the presence of calcium.

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

Similarity. Belongs to the synaptobrevin family.

Isoforms (2)

UniProt ID	Names	Canonical?
O75379-1	1	yes
O75379-2	2

RefSeq proteins (2): NP_001172056, NP_003753* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001388	Synaptobrevin-like	Family
IPR042855	V_SNARE_CC	Domain
IPR042887	VAMP4	Family

Pfam: PF00957

UniProt features (10 total): topological domain 2, modified residue 2, chain 1, transmembrane region 1, domain 1, region of interest 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O75379-F1	81.23	0.48

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): 17, 30

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-6811440	Retrograde transport at the Trans-Golgi-Network
R-HSA-8856825	Cargo recognition for clathrin-mediated endocytosis
R-HSA-8856828	Clathrin-mediated endocytosis

MSigDB gene sets: 243 (showing top): GSE45365_NK_CELL_VS_CD8_TCELL_DN, GOBP_RESPONSE_TO_PEPTIDE, TGCACTT_MIR519C_MIR519B_MIR519A, GOBP_VESICLE_ORGANIZATION, MORF_ATRX, GOBP_MEMBRANE_FUSION, GOCC_CELL_SURFACE, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT, GTGCCTT_MIR506, GOBP_GOLGI_TO_PLASMA_MEMBRANE_TRANSPORT, GOCC_TRANS_GOLGI_NETWORK, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM

GO Biological Process (12): synaptic vesicle to endosome fusion (GO:0016189), endocytic recycling (GO:0032456), SNARE complex assembly (GO:0035493), regulation of Golgi to plasma membrane protein transport (GO:0042996), Golgi to plasma membrane protein transport (GO:0043001), cellular response to type II interferon (GO:0071346), Golgi ribbon formation (GO:0090161), neurotransmitter receptor transport, endosome to postsynaptic membrane (GO:0098887), vesicle-mediated transport in synapse (GO:0099003), regulation of synaptic vesicle endocytosis (GO:1900242), vesicle-mediated transport (GO:0016192), vesicle-mediated transport to the plasma membrane (GO:0098876)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (18): Golgi membrane (GO:0000139), lysosome (GO:0005764), endosome (GO:0005768), Golgi apparatus (GO:0005794), trans-Golgi network (GO:0005802), plasma membrane (GO:0005886), cell surface (GO:0009986), transport vesicle (GO:0030133), clathrin-coated endocytic vesicle membrane (GO:0030669), SNARE complex (GO:0031201), trans-Golgi network membrane (GO:0032588), phagocytic vesicle (GO:0045335), presynaptic endosome membrane (GO:0098954), glutamatergic synapse (GO:0098978), membrane (GO:0016020), endocytic vesicle (GO:0030139), cytoplasmic vesicle membrane (GO:0030659), bounding membrane of organelle (GO:0098588)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Intra-Golgi and retrograde Golgi-to-ER traffic	1
Clathrin-mediated endocytosis	1
Membrane Trafficking	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasmic vesicle	4
endomembrane system	3
vesicle-mediated transport	2
synapse	2
cytoplasm	2
cellular anatomical structure	2
organelle membrane	2
endosome organization	1
organelle fusion	1
synaptic vesicle endosomal processing	1
endosomal transport	1
vesicle-mediated transport to the plasma membrane	1
vesicle fusion	1
protein-containing complex assembly	1
Golgi to plasma membrane protein transport	1
regulation of protein transport	1
regulation of vesicle-mediated transport	1
regulation of protein localization to plasma membrane	1
Golgi to plasma membrane transport	1
protein transport	1
establishment of protein localization to plasma membrane	1
protein localization to plasma membrane	1
response to type II interferon	1
cellular response to cytokine stimulus	1
Golgi organization	1
intercellular transport	1
neurotransmitter receptor transport to postsynaptic membrane	1
neurotransmitter receptor transport, endosome to plasma membrane	1
regulation of endocytosis	1
synaptic vesicle endocytosis	1
regulation of synaptic vesicle recycling	1
transport	1
cellular process	1
exocytosis	1
localization within membrane	1
binding	1
Golgi apparatus	1
bounding membrane of organelle	1
lytic vacuole	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1444 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
VAMP4	STX6	O43752	999
VAMP4	VTI1A	Q96AJ9	993
VAMP4	STX16	O14662	991
VAMP4	VTI1B	Q9UEU0	873
VAMP4	STX1A	Q16623	836
VAMP4	VAMP7	P51809	835
VAMP4	STX5	Q13190	835
VAMP4	SNAP23	O00161	831
VAMP4	VPS53	Q5VIR6	816
VAMP4	STX12	Q86Y82	781
VAMP4	VPS54	Q9P1Q0	761
VAMP4	STX10	O60499	760
VAMP4	YKT6	O15498	743
VAMP4	SNAP29	O95721	714
VAMP4	STX4	Q12846	694

IntAct

172 interactions, top by confidence:

A	B	Type	Score
STX12	STX6	psi-mi:“MI:0915”(physical association)	0.860
STX12	STX6	psi-mi:“MI:0914”(association)	0.860
STX4	VAMP4	psi-mi:“MI:0915”(physical association)	0.830
VAMP4	STX4	psi-mi:“MI:0915”(physical association)	0.830
NAPA	SNAP23	psi-mi:“MI:0914”(association)	0.780
VAMP4	STX6	psi-mi:“MI:0915”(physical association)	0.670
STX5	GOSR2	psi-mi:“MI:0914”(association)	0.670
STX7	SNAP23	psi-mi:“MI:0914”(association)	0.640
STX12	SNAP23	psi-mi:“MI:0914”(association)	0.640
VAMP4	STX7	psi-mi:“MI:0914”(association)	0.640
KASH5	VAMP4	psi-mi:“MI:0915”(physical association)	0.560
VAMP4	KASH5	psi-mi:“MI:0915”(physical association)	0.560
VAMP4	SNAP47	psi-mi:“MI:0915”(physical association)	0.560
VAMP4		psi-mi:“MI:0915”(physical association)	0.560
VAMP4	LDLRAD1	psi-mi:“MI:0915”(physical association)	0.560
VAMP4	STX1A	psi-mi:“MI:0915”(physical association)	0.560
VAMP4	MFF	psi-mi:“MI:0915”(physical association)	0.560
STX16	VAMP4	psi-mi:“MI:0915”(physical association)	0.560
VAMP4	MTIF3	psi-mi:“MI:0915”(physical association)	0.560
VAMP4	SAR1A	psi-mi:“MI:0915”(physical association)	0.560
VAMP4	TMEM205	psi-mi:“MI:0915”(physical association)	0.560
VAMP4	TMEM51	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (229): VAMP4 (Two-hybrid), SNAP29 (Two-hybrid), BCL2L13 (Two-hybrid), CCDC155 (Two-hybrid), STX6 (Affinity Capture-Western), STX7 (Affinity Capture-Western), STX8 (Affinity Capture-Western), VAMP4 (Affinity Capture-MS), VAMP4 (Affinity Capture-MS), VAMP4 (Affinity Capture-MS), VAMP4 (Affinity Capture-MS), VAMP4 (Affinity Capture-MS), VAMP4 (Affinity Capture-MS), VAMP4 (Two-hybrid), VAMP4 (Proximity Label-MS)

ESM2 similar proteins: G3V7P1, O08522, O14662, O15400, O22151, O43752, O49377, O60499, O64791, O70257, O70439, O70480, O75379, O88384, O88630, O88983, O95249, P58200, Q08851, Q08DB5, Q13190, Q2KIU0, Q2TBU3, Q32L97, Q3T075, Q3ZBT5, Q5R602, Q5R6Q2, Q5RBL6, Q5RBW6, Q5RF94, Q5SRX1, Q5ZL19, Q62931, Q63635, Q86Y82, Q8BVI5, Q8K1E0, Q944A9, Q946Y7

Diamond homologs: O02495, O48850, O49377, O70404, O70480, O75379, O95183, P13701, P18489, P23763, P31109, P33328, P34351, P35589, P47192, P47193, P47194, P63024, P63025, P63026, P63027, P63044, P63045, Q0V7N0, Q12255, Q15836, Q27236, Q2KHY2, Q2KJD2, Q32L97, Q3T0Y8, Q4R8T0, Q5REQ5, Q60WU2, Q62442, Q63666, Q6TMJ9, Q92356, Q9BV40, Q9FMR5

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
CSNK2A1	up-regulates	VAMP4	phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 88 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	10	51.9×	6e-13
Retrograde transport at the Trans-Golgi-Network	8	35.1×	6e-09
trans-Golgi Network Vesicle Budding	6	30.4×	2e-06
Intra-Golgi and retrograde Golgi-to-ER traffic	9	18.9×	5e-08
COPII-mediated vesicle transport	5	16.3×	5e-04
COPI-mediated anterograde transport	5	11.0×	2e-03
Membrane Trafficking	13	9.6×	4e-08
Vesicle-mediated transport	13	9.1×	5e-08

GO biological processes:

GO term	Partners	Fold	FDR
obsolete vesicle docking	11	108.0×	1e-18
vesicle fusion	12	92.6×	4e-19
membrane fusion	6	48.0×	2e-07
intra-Golgi vesicle-mediated transport	5	33.8×	2e-05
retrograde transport, endosome to Golgi	8	21.1×	2e-07
endocytic recycling	6	20.6×	2e-05
exocytosis	10	19.5×	8e-09
intracellular protein transport	16	13.3×	6e-12

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	16
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1605 predictions. Top by Δscore:

Variant	Effect	Δscore
1:171704535:C:CC	acceptor_gain	1.0000
1:171706359:ATAC:A	donor_loss	1.0000
1:171706360:TACTT:T	donor_loss	1.0000
1:171706361:AC:A	donor_loss	1.0000
1:171706362:CTT:C	donor_loss	1.0000
1:171706363:TTAC:T	donor_loss	1.0000
1:171706364:TA:T	donor_loss	1.0000
1:171706365:A:AC	donor_gain	1.0000
1:171706365:ACTGA:A	donor_loss	1.0000
1:171706366:C:CA	donor_gain	1.0000
1:171706366:CT:C	donor_gain	1.0000
1:171706366:CTG:C	donor_gain	1.0000
1:171706366:CTGAT:C	donor_gain	1.0000
1:171706417:ATCTA:A	acceptor_loss	1.0000
1:171706418:TCTA:T	acceptor_loss	1.0000
1:171706419:C:CC	acceptor_gain	1.0000
1:171706419:CTAC:C	acceptor_loss	1.0000
1:171706420:T:C	acceptor_loss	1.0000
1:171709661:TTA:T	donor_loss	1.0000
1:171709662:TACTT:T	donor_loss	1.0000
1:171709663:A:AC	donor_gain	1.0000
1:171709664:C:CC	donor_gain	1.0000
1:171709664:CT:C	donor_gain	1.0000
1:171709664:CTTTG:C	donor_gain	1.0000
1:171709741:CTTT:C	acceptor_gain	1.0000
1:171709742:TTT:T	acceptor_gain	1.0000
1:171709745:C:CC	acceptor_gain	1.0000
1:171709751:C:CT	acceptor_gain	1.0000
1:171709754:A:C	acceptor_gain	1.0000
1:171710708:CTGTA:C	donor_loss	1.0000

AlphaMissense

941 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:171709727:C:G	A95P	0.999
1:171710728:A:G	L84P	0.999
1:171709716:A:C	F98L	0.998
1:171709716:A:T	F98L	0.998
1:171709718:A:G	F98L	0.998
1:171710717:A:G	S88P	0.998
1:171709738:A:G	L91S	0.997
1:171710769:A:C	N70K	0.997
1:171710769:A:T	N70K	0.997
1:171710776:T:G	Q68P	0.997
1:171710779:A:T	M67K	0.997
1:171709717:A:G	F98S	0.996
1:171709736:A:G	S92P	0.996
1:171710737:A:G	L81P	0.996
1:171710770:T:A	N70I	0.996
1:171710779:A:C	M67R	0.996
1:171738400:A:C	F5L	0.996
1:171738400:A:T	F5L	0.996
1:171738402:A:G	F5L	0.996
1:171709696:A:G	L105P	0.995
1:171710748:T:A	R77S	0.995
1:171710748:T:G	R77S	0.995
1:171710778:C:A	M67I	0.995
1:171710778:C:G	M67I	0.995
1:171710778:C:T	M67I	0.995
1:171710803:T:G	Q59P	0.995
1:171710812:A:T	V56D	0.995
1:171709717:A:C	F98C	0.994
1:171709726:G:T	A95E	0.994
1:171710771:T:A	N70Y	0.994

dbSNP variants (sampled 300 via entrez): RS1000040510 (1:171719639 A>G,T), RS1000078816 (1:171742021 G>A,C,T), RS1000147804 (1:171724879 A>G), RS1000183833 (1:171711908 T>C), RS1000236190 (1:171711599 C>T), RS1000272593 (1:171715956 G>C), RS1000582418 (1:171729925 T>C), RS1000658440 (1:171723670 C>G), RS1000727190 (1:171715641 C>A,T), RS1000799043 (1:171700951 C>T), RS1000855610 (1:171709154 G>T), RS1000860825 (1:171704729 ACATTGG>A), RS1000906083 (1:171742944 G>A), RS1000954883 (1:171730284 C>T), RS1000958376 (1:171743636 C>T)

Disease associations

OMIM: gene MIM:606909 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST002760_1	Hippocampal atrophy	4.000000e-06
GCST003075_102	Cognitive decline rate in late mild cognitive impairment	1.000000e-07
GCST003075_103	Cognitive decline rate in late mild cognitive impairment	7.000000e-07
GCST003075_2	Cognitive decline rate in late mild cognitive impairment	1.000000e-06
GCST003075_8	Cognitive decline rate in late mild cognitive impairment	2.000000e-07
GCST009325_81	Parkinson’s disease or first degree relation to individual with Parkinson’s disease	4.000000e-09
GCST009391_917	Metabolite levels	8.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0005039	hippocampal atrophy
EFO:0007710	cognitive decline measurement
EFO:0010442	triacylglycerol 58:8 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance, increases expression	4
Valproic Acid	increases expression, affects expression, decreases expression	3
Cyclosporine	increases expression	3
Air Pollutants	decreases expression, increases abundance	2
Cadmium Chloride	decreases expression, increases abundance	2
GSK-J4	increases expression	1
FR900359	increases phosphorylation	1
bisphenol F	affects cotreatment, increases expression	1
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, increases expression	1
deoxynivalenol	increases expression	1
arsenite	affects binding, increases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
cobaltous chloride	increases expression	1
butyraldehyde	decreases expression	1
manganese chloride	increases abundance, increases expression	1
pentanal	decreases expression	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
abrine	increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	increases expression	1
jinfukang	decreases expression	1
MT19c compound	increases expression	1
Temozolomide	affects response to substance	1
Arsenic Trioxide	increases expression	1
Arsenic	increases abundance, increases expression	1
Cadmium	decreases expression, increases abundance	1
Carmustine	affects response to substance	1

Clinical trials (associated diseases)

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