SVOP

Summary

SVOP (SV2 related protein, HGNC:25417) is a protein-coding gene on chromosome 12q24.11, encoding Synaptic vesicle 2-related protein (Q8N4V2).

Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport and xenobiotic transport. Predicted to be located in synaptic vesicle. Predicted to be active in synaptic vesicle membrane.

Source: NCBI Gene 55530 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_018711

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25417
Approved symbol	SVOP
Name	SV2 related protein
Location	12q24.11
Locus type	gene with protein product
Status	Approved
Aliases	DKFZp761H039, SLC22B4
Ensembl gene	ENSG00000166111
Ensembl biotype	protein_coding
OMIM	611699
Entrez	55530

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 2 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000546618, ENST00000548229, ENST00000550436, ENST00000551211, ENST00000610966

RefSeq mRNA: 1 — MANE Select: NM_018711 NM_018711

CCDS: CCDS73520

Canonical transcript exons

ENST00000610966 — 16 exons

Exon	Start	End
ENSE00000938126	108918043	108918124
ENSE00000938127	108915783	108915872
ENSE00001099889	108938827	108938955
ENSE00001099893	108922690	108922797
ENSE00001099895	108937264	108937337
ENSE00001099905	108934195	108934271
ENSE00001222360	108919675	108919786
ENSE00001688711	108977398	108977496
ENSE00001759336	108978578	108978663
ENSE00001773173	108940784	108940909
ENSE00002414918	109020834	109021068
ENSE00002587072	108907741	108912741
ENSE00003517814	108960923	108961047
ENSE00003551928	108945103	108945166
ENSE00003678511	108972405	108972476
ENSE00003723344	108983601	108983761

Expression profiles

Bgee: expression breadth ubiquitous, 136 present calls, max score 98.43.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 2.2766 / max 172.2434, expressed in 159 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
133179	0.9637	123
133181	0.5404	116
133180	0.3820	102
133178	0.2095	68
133176	0.1393	48
133177	0.0417	30

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
endothelial cell	CL:0000115	98.43	gold quality
middle temporal gyrus	UBERON:0002771	93.92	gold quality
Brodmann (1909) area 23	UBERON:0013554	93.19	gold quality
Brodmann (1909) area 46	UBERON:0006483	92.36	gold quality
prefrontal cortex	UBERON:0000451	91.46	gold quality
superior frontal gyrus	UBERON:0002661	91.09	gold quality
frontal cortex	UBERON:0001870	90.23	gold quality
cortical plate	UBERON:0005343	89.77	gold quality
entorhinal cortex	UBERON:0002728	89.03	gold quality
neocortex	UBERON:0001950	88.74	gold quality
right frontal lobe	UBERON:0002810	88.03	gold quality
postcentral gyrus	UBERON:0002581	87.89	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	87.68	gold quality
cerebral cortex	UBERON:0000956	87.42	gold quality
parietal lobe	UBERON:0001872	87.06	gold quality
Brodmann (1909) area 9	UBERON:0013540	87.00	gold quality
cerebellar cortex	UBERON:0002129	86.34	gold quality
cerebellum	UBERON:0002037	86.32	gold quality
cerebellar hemisphere	UBERON:0002245	86.27	gold quality
right hemisphere of cerebellum	UBERON:0014890	86.22	gold quality
anterior cingulate cortex	UBERON:0009835	85.47	gold quality
primary visual cortex	UBERON:0002436	85.29	gold quality
cerebellar vermis	UBERON:0004720	84.38	gold quality
occipital lobe	UBERON:0002021	83.32	gold quality
Ammon’s horn	UBERON:0001954	83.02	gold quality
forebrain	UBERON:0001890	83.01	gold quality
brain	UBERON:0000955	82.92	gold quality
temporal lobe	UBERON:0001871	82.81	gold quality
nucleus accumbens	UBERON:0001882	82.66	gold quality
islet of Langerhans	UBERON:0000006	81.24	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-5061	yes	9.81
E-GEOD-84465	yes	6.50
E-ANND-3	yes	5.36

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

127 targeting SVOP, 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-371B-5P	99.99	75.34	4759
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-4496	99.88	68.89	2236
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-659-3P	99.85	70.69	1620
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-4420	99.82	70.08	1624
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-181B-2-3P	99.81	70.06	1646
HSA-MIR-181B-3P	99.81	70.06	1646
HSA-MIR-548AJ-5P	99.78	71.12	3085

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	svopa	ENSDARG00000056833
mus_musculus	Svop	ENSMUSG00000042078
rattus_norvegicus	Svop	ENSRNOG00000000693
drosophila_melanogaster	CG4324	FBGN0034956
caenorhabditis_elegans		WBGENE00014021

Paralogs (22): SLC22A16 (ENSG00000004809), SLC22A17 (ENSG00000092096), SLC22A2 (ENSG00000112499), SLC22A7 (ENSG00000137204), SLC22A23 (ENSG00000137266), SLC22A14 (ENSG00000144671), SLC22A3 (ENSG00000146477), SLC22A8 (ENSG00000149452), SLC22A9 (ENSG00000149742), SVOPL (ENSG00000157703), SLC22A15 (ENSG00000163393), SLC22A11 (ENSG00000168065), SLC22A13 (ENSG00000172940), SLC22A1 (ENSG00000175003), SLC22A10 (ENSG00000184999), SLC22A25 (ENSG00000196600), SLC22A4 (ENSG00000197208), SLC22A5 (ENSG00000197375), SLC22A24 (ENSG00000197658), SLC22A12 (ENSG00000197891), SLC22A6 (ENSG00000197901), SLC22A31 (ENSG00000259803)

Protein

Protein identifiers

Synaptic vesicle 2-related protein — Q8N4V2 (reviewed: Q8N4V2)

All UniProt accessions (3): Q8N4V2, H0YHK4, H0YHQ5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasmic vesicle. Secretory vesicle. Synaptic vesicle membrane.

Similarity. Belongs to the major facilitator superfamily.

RefSeq proteins (1): NP_061181* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004749	Orgcat_transp/SVOP	Family
IPR005828	MFS_sugar_transport-like	Family
IPR011701	MFS	Family
IPR020846	MFS_dom	Domain
IPR036259	MFS_trans_sf	Homologous_superfamily
IPR047969	SVOP-like_MFS_dom	Domain

Pfam: PF00083, PF07690

UniProt features (29 total): topological domain 13, transmembrane region 12, modified residue 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N4V2-F1	78.87	0.51

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): 25, 31, 542

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 89 (showing top): ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOBP_TRANSMEMBRANE_TRANSPORT, GOCC_EXOCYTIC_VESICLE, GOCC_SECRETORY_VESICLE, GOCC_SYNAPSE, GOCC_PLASMA_MEMBRANE_REGION, GOCC_PRESYNAPSE, GOCC_TRANSPORT_VESICLE_MEMBRANE, GOCC_BASAL_PART_OF_CELL, chr12q24, GOMF_TRANSPORTER_ACTIVITY, MEISSNER_NPC_HCP_WITH_H3K4ME2, CACTGCC_MIR34A_MIR34C_MIR449, MIKKELSEN_MEF_HCP_WITH_H3K27ME3, KAMMINGA_SENESCENCE

GO Biological Process (2): xenobiotic transport (GO:0042908), transmembrane transport (GO:0055085)

GO Molecular Function (2): transmembrane transporter activity (GO:0022857), protein binding (GO:0005515)

GO Cellular Component (6): synaptic vesicle (GO:0008021), basal plasma membrane (GO:0009925), synaptic vesicle membrane (GO:0030672), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410), synapse (GO:0045202)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transport	2
cellular process	1
transporter activity	1
transmembrane transport	1
binding	1
exocytic vesicle	1
presynapse	1
basal part of cell	1
plasma membrane region	1
synaptic vesicle	1
exocytic vesicle membrane	1
cellular anatomical structure	1
cytoplasm	1
intracellular vesicle	1
cell junction	1

Protein interactions and networks

STRING

1116 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SVOP	SLC67A2	Q8NBP5	676
SVOP	SLC75A1	Q14728	628
SVOP	MFSD11	O43934	620
SVOP	UNC93A	Q86WB7	618
SVOP	SLC61A1	Q6N075	604
SVOP	SPNS1	Q9H2V7	564
SVOP	SLC68A1	Q14CX5	528
SVOP	SPNS3	Q6ZMD2	523
SVOP	AMER3	Q8N944	512
SVOP	MFSD6L	Q8IWD5	493
SVOP	SLC71A1	Q96MC6	492
SVOP	SLC38A12	Q8NE00	489
SVOP	SLC33A2	Q96ES6	485
SVOP	UNC93B1	Q9H1C4	479
SVOP	CCNP	Q9H8S5	478

IntAct

14 interactions, top by confidence:

A	B	Type	Score
SVOP	FXYD6	psi-mi:“MI:0915”(physical association)	0.600
SVOP	GLP1R	psi-mi:“MI:0915”(physical association)	0.540
GLP1R	SVOP	psi-mi:“MI:0403”(colocalization)	0.540
SVOP	CCR2	psi-mi:“MI:0915”(physical association)	0.370
SVOP	CYSLTR2	psi-mi:“MI:0915”(physical association)	0.370
SVOP	TAAR1	psi-mi:“MI:0915”(physical association)	0.370
SVOP	CREB3	psi-mi:“MI:0915”(physical association)	0.370
SVOP	PGRMC1	psi-mi:“MI:0914”(association)	0.350
FXYD6	SVOP	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (62): SVOP (Biochemical Activity), SVOP (Affinity Capture-MS), SVOP (Two-hybrid), SVOP (Two-hybrid), SVOP (Two-hybrid), SVOP (Two-hybrid), SVOP (Two-hybrid), ABHD12 (Affinity Capture-MS), ALDH3A2 (Affinity Capture-MS), ATP5I (Affinity Capture-MS), ATP5J (Affinity Capture-MS), CERK (Affinity Capture-MS), CLPTM1 (Affinity Capture-MS), CNNM1 (Affinity Capture-MS), COX5A (Affinity Capture-MS)

ESM2 similar proteins: A0A2K2BF92, A2SWM2, B0JZE1, B8AF63, E2RFJ3, F1NCD6, O80605, P53988, P54219, P57057, Q01818, Q08DX7, Q0IHM1, Q17QZ3, Q1JP63, Q2XWK0, Q2YDU8, Q3TIT8, Q58CV5, Q5F3N0, Q5M7K3, Q5R5T8, Q5TF39, Q5U3U7, Q5ZIT9, Q640L2, Q6DEJ6, Q6YK44, Q7SY29, Q7ZU13, Q8AVC3, Q8BFT9, Q8BH31, Q8K078, Q8N4V2, Q8NA29, Q8NCC5, Q8NHS3, Q8R070, Q8R090

Diamond homologs: A0A1B5L780, A0A1D8PH98, A0A8F4NW86, B2GV36, J9VHZ4, J9VLA6, J9VLY3, J9VTS6, J9VX18, J9VXV2, J9W1D0, P28568, P30605, P30606, P87110, Q04301, Q10286, Q1JP63, Q2XWK0, Q39524, Q46909, Q51955, Q5R5T8, Q6A4L0, Q6FFF7, Q8BFT9, Q8LPQ8, Q8N4V2, Q940M4, Q9I6Q3, Q9LHQ6, Q9SD00, Q9WV38, A6NK97, A6QLW8, A7MBE0, A9CB25, O02713, O08966, O15244

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

2438 predictions. Top by Δscore:

Variant	Effect	Δscore
12:108915778:CCTA:C	donor_loss	1.0000
12:108915782:C:CG	donor_loss	1.0000
12:108922796:GA:G	acceptor_gain	1.0000
12:108922797:AC:A	acceptor_loss	1.0000
12:108922798:C:CC	acceptor_gain	1.0000
12:108922804:T:C	acceptor_gain	1.0000
12:108934193:A:AC	donor_gain	1.0000
12:108934194:C:CC	donor_gain	1.0000
12:108940782:A:AC	donor_gain	1.0000
12:108940783:C:CC	donor_gain	1.0000
12:108940783:CGAAA:C	donor_gain	1.0000
12:108960921:A:AC	donor_gain	1.0000
12:108960922:C:CC	donor_gain	1.0000
12:108960922:CGA:C	donor_gain	1.0000
12:108972403:A:AC	donor_gain	1.0000
12:108972404:C:CC	donor_gain	1.0000
12:108978498:T:TA	donor_gain	1.0000
12:109020832:A:AC	donor_gain	1.0000
12:109020833:C:CC	donor_gain	1.0000
12:109020833:CGG:C	donor_gain	1.0000
12:109020847:G:C	donor_gain	1.0000
12:108912539:T:A	donor_gain	0.9900
12:108912583:T:TA	donor_gain	0.9900
12:108912612:C:CA	donor_gain	0.9900
12:108915874:TGAAA:T	acceptor_loss	0.9900
12:108918093:T:C	acceptor_gain	0.9900
12:108918093:T:TC	acceptor_gain	0.9900
12:108918120:CATTT:C	acceptor_gain	0.9900
12:108919671:CTACC:C	donor_loss	0.9900
12:108919672:TACCT:T	donor_loss	0.9900

AlphaMissense

3542 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:108915811:C:T	G471D	1.000
12:108915812:C:G	G471R	1.000
12:108915838:C:T	G462D	1.000
12:108915839:C:G	G462R	1.000
12:108915844:C:T	G460D	1.000
12:108919748:G:T	R399S	1.000
12:108934245:C:T	G333E	1.000
12:108934246:C:A	G333W	1.000
12:108938880:C:G	A282P	1.000
12:108938891:A:G	L278S	1.000
12:108938941:A:C	S261R	1.000
12:108938941:A:T	S261R	1.000
12:108938943:T:G	S261R	1.000
12:108940893:C:T	G220E	1.000
12:108940894:C:A	G220W	1.000
12:108940894:C:G	G220R	1.000
12:108940894:C:T	G220R	1.000
12:108940903:A:G	W217R	1.000
12:108940903:A:T	W217R	1.000
12:108945143:A:G	L201P	1.000
12:108945158:A:G	L196P	1.000
12:108960938:C:T	G188E	1.000
12:108960944:C:T	G186E	1.000
12:108960951:C:G	G184R	1.000
12:108972411:C:A	R149S	1.000
12:108972411:C:G	R149S	1.000
12:108972412:C:A	R149M	1.000
12:108972412:C:G	R149T	1.000
12:108972415:C:A	G148V	1.000
12:108972415:C:T	G148D	1.000

dbSNP variants (sampled 300 via entrez): RS1000002660 (12:108936852 C>T), RS1000036822 (12:108936583 C>T), RS1000053015 (12:108939434 A>C,G), RS1000082911 (12:108981480 A>G), RS1000123028 (12:108973506 C>T), RS1000160558 (12:108915926 C>T), RS1000182878 (12:108971439 A>G), RS1000191459 (12:109003368 A>G), RS1000214269 (12:109003619 T>A), RS1000233061 (12:108924365 G>A), RS1000291256 (12:109019112 T>C), RS1000316766 (12:108956010 C>G,T), RS1000333141 (12:109009825 G>A), RS1000343162 (12:108932993 C>T), RS1000406254 (12:109019514 G>C,T)

Disease associations

OMIM: gene MIM:611699 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs3918305	SVOP		0.00	0

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases methylation, increases expression	2
CGP 52608	affects binding, increases reaction	1
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	decreases methylation, increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Smoke	decreases expression	1
Tretinoin	increases expression	1

Clinical trials (associated diseases)

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