SNX2

Summary

SNX2 (sorting nexin 2, HGNC:11173) is a protein-coding gene on chromosome 5q23.2, encoding Sorting nexin-2 (O60749). Involved in several stages of intracellular trafficking.

This gene belongs to the sorting nexin family whose members contain the phosphoinositide-binding phox (PX) domain. The encoded protein is a component of the retromer complex which plays a role in protein sorting in the endocytic pathway. This protein may form oligomeric complexes with other family members. Alternate splicing results in multiple transcript variants of this gene. Pseudogenes associated with this gene are located on chromosomes 1 and 7.

Source: NCBI Gene 6643 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 78 total
• Druggable target: yes
• MANE Select transcript: NM_003100

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:11173
Approved symbol	SNX2
Name	sorting nexin 2
Location	5q23.2
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000205302
Ensembl biotype	protein_coding
OMIM	605929
Entrez	6643

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 16 protein_coding, 6 retained_intron, 3 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000379516, ENST00000505854, ENST00000505934, ENST00000506847, ENST00000506874, ENST00000507321, ENST00000507852, ENST00000509281, ENST00000510372, ENST00000511365, ENST00000512394, ENST00000514030, ENST00000514949, ENST00000889594, ENST00000925948, ENST00000925949, ENST00000958472, ENST00000958473, ENST00000958474, ENST00000958475, ENST00000958476, ENST00000958477, ENST00000958478, ENST00000958479, ENST00000958480, ENST00000958481

RefSeq mRNA: 2 — MANE Select: NM_003100 NM_001278199, NM_003100

CCDS: CCDS34217, CCDS64234

Canonical transcript exons

ENST00000379516 — 15 exons

Exon	Start	End
ENSE00001481376	122829598	122834543
ENSE00002021284	122775080	122775211
ENSE00003520619	122795266	122795383
ENSE00003548953	122818818	122819023
ENSE00003551121	122801869	122801935
ENSE00003551423	122827575	122827646
ENSE00003551506	122808277	122808355
ENSE00003560111	122799692	122799855
ENSE00003576508	122827379	122827459
ENSE00003592904	122826050	122826193
ENSE00003615343	122816915	122817028
ENSE00003632171	122803472	122803613
ENSE00003633893	122815896	122815971
ENSE00003646806	122802081	122802124
ENSE00003662753	122817280	122817373

Expression profiles

Bgee: expression breadth ubiquitous, 291 present calls, max score 98.93.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 64.4522 / max 681.5538, expressed in 1822 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
58211	64.0973	1822
58212	0.3549	101

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
monocyte	CL:0000576	98.93	gold quality
mononuclear cell	CL:0000842	98.71	gold quality
leukocyte	CL:0000738	98.63	gold quality
calcaneal tendon	UBERON:0003701	98.16	gold quality
islet of Langerhans	UBERON:0000006	98.01	gold quality
ventricular zone	UBERON:0003053	97.96	gold quality
gall bladder	UBERON:0002110	97.63	gold quality
rectum	UBERON:0001052	97.46	gold quality
ganglionic eminence	UBERON:0004023	97.35	gold quality
descending thoracic aorta	UBERON:0002345	97.21	gold quality
tendon	UBERON:0000043	97.12	gold quality
popliteal artery	UBERON:0002250	97.12	gold quality
tibial artery	UBERON:0007610	97.11	gold quality
vermiform appendix	UBERON:0001154	97.10	gold quality
right coronary artery	UBERON:0001625	97.10	gold quality
spleen	UBERON:0002106	97.05	gold quality
right lobe of thyroid gland	UBERON:0001119	97.00	gold quality
left lobe of thyroid gland	UBERON:0001120	96.97	gold quality
left ovary	UBERON:0002119	96.87	gold quality
right ovary	UBERON:0002118	96.86	gold quality
aorta	UBERON:0000947	96.80	gold quality
right lung	UBERON:0002167	96.79	gold quality
adrenal tissue	UBERON:0018303	96.76	gold quality
thyroid gland	UBERON:0002046	96.71	gold quality
right uterine tube	UBERON:0001302	96.65	gold quality
left coronary artery	UBERON:0001626	96.58	gold quality
thoracic aorta	UBERON:0001515	96.51	gold quality
granulocyte	CL:0000094	96.50	gold quality
metanephros cortex	UBERON:0010533	96.50	gold quality
ascending aorta	UBERON:0001496	96.46	gold quality

Single-cell (SCXA)

Detected in 12 experiment(s), a significant marker in 9.

Experiment	Marker?	Max mean expression
E-HCAD-4	yes	104.75
E-CURD-122	yes	71.97
E-CURD-88	yes	46.31
E-MTAB-6701	yes	45.85
E-CURD-112	yes	42.36
E-MTAB-9467	yes	30.06
E-MTAB-9221	yes	20.96
E-HCAD-13	yes	20.77
E-MTAB-3929	no	869.65
E-GEOD-100618	no	763.95
E-MTAB-7249	no	404.63
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

196 targeting SNX2, 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-6867-5P	100.00	82.21	3464
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-511-3P	99.99	68.85	1467
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-499A-5P	99.98	70.79	1323
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-302C-5P	99.97	72.56	3642
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-3658	99.96	73.87	4379

Literature-anchored findings (GeneRIF, showing 11)

• Examined the effect of a PX domain-mutated SNX2 that is defective in vesicle localization on EGFR trafficking. (PMID:14978220)
• The N-terminal domain of Abs interacts with the phox homology (PX) domain of SNX2 suggesting that PX domains may also participate in protein-protein interaction (PMID:15690390)
• Data suggest that sorting nexin-2 is not essential for the regulation of endosome-to-trans Golgi network retrieval of the cation-independent mannose 6-phosphate receptor. (PMID:16179610)
• These observations indicate that the mammalian retromer complex assembles by sequential association of SNX1/2 and Vps26-Vps29-Vps35 subcomplexes on endosomal membranes and that SNX1 and SNX2 play interchangeable but essential roles. (PMID:17101778)
• study indicates that hVps34 and its product PI(3)P are involved in endosome to Golgi transport of ricin, and that SNX2 and SNX4 are likely to be effectors in this pathway (PMID:17319803)
• SNX1 and SNX2 interact with the Rac1 and RhoG guanine nucleotide exchange factor Kalirin-7. Overexpression of SNX1 or SNX2 and Kalirin-7 partially redistributes both SNXs to the plasma membrane, and results in RhoG-dependent lamellipodia formation. (PMID:20604901)
• Silencing of SNX2 markedly alters sensitivity to anticancer drugs targeted to c-Met. (PMID:23360489)
• SNX2 is highly expressed in 73.3% Graves disease patients and in 93.8% thyroid nodule patients. (PMID:23531855)
• Host Retromer Protein Sorting Nexin 2 Interacts with Human Respiratory Syncytial Virus Structural Proteins and is Required for Efficient Viral Production. (PMID:32994321)
• Human sorting nexin 2 protein interacts with Influenza A virus PA protein and has a negative regulatory effect on the virus replication. (PMID:34817777)
• Spatiotemporal regulation of the hepatocyte growth factor receptor MET activity by sorting nexins 1/2 in HCT116 colorectal cancer cells. (PMID:38836326)

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	snx2	ENSDARG00000104128
mus_musculus	Snx2	ENSMUSG00000034484
rattus_norvegicus	Snx2	ENSRNOG00000017832
drosophila_melanogaster	Snx1	FBGN0031534
drosophila_melanogaster	Snx6	FBGN0032005
caenorhabditis_elegans		WBGENE00004927
caenorhabditis_elegans		WBGENE00013354

Paralogs (15): SNX11 (ENSG00000002919), SNX1 (ENSG00000028528), SNX10 (ENSG00000086300), SNX5 (ENSG00000089006), SNX8 (ENSG00000106266), SNX3 (ENSG00000112335), SNX4 (ENSG00000114520), SNX6 (ENSG00000129515), SNX9 (ENSG00000130340), SNX12 (ENSG00000147164), SNX30 (ENSG00000148158), SNX7 (ENSG00000162627), SNX32 (ENSG00000172803), SNX33 (ENSG00000173548), SNX18 (ENSG00000178996)

Protein

Protein identifiers

Sorting nexin-2 — O60749 (reviewed: O60749)

Alternative names: Transformation-related gene 9 protein

All UniProt accessions (3): D6RBT1, O60749, D6RC15

UniProt curated annotations — full annotation on UniProt →

Function. Involved in several stages of intracellular trafficking. Interacts with membranes containing phosphatidylinositol 3-phosphate (PtdIns(3P)) or phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2). Acts in part as component of the retromer membrane-deforming SNX-BAR subcomplex. The SNX-BAR retromer mediates retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN) and is involved in endosome-to-plasma membrane transport for cargo protein recycling. The SNX-BAR subcomplex functions to deform the donor membrane into a tubular profile called endosome-to-TGN transport carrier (ETC). Can sense membrane curvature and has in vitro vesicle-to-membrane remodeling activity. Required for retrograde endosome-to-TGN transport of TGN38. Promotes KALRN- and RHOG-dependent but retromer-independent membrane remodeling such as lamellipodium formation; the function is dependent on GEF activity of KALRN.

Subunit / interactions. Predominantly forms heterodimers with BAR domain-containing sorting nexins SNX5, SNX6 and SNX32; can self-associate to form homodimers. The heterodimers are proposed to self-assemble into helical arrays on the membrane to stabilize and expand local membrane curvature underlying endosomal tubule formation. Thought to be a component of the originally described retromer complex (also called SNX-BAR retromer) which is a pentamer containing the heterotrimeric retromer cargo-selective complex (CSC), also described as vacuolar protein sorting subcomplex (VPS), and a heterodimeric membrane-deforming subcomplex formed between SNX1 or SNX2 and SNX5 or SNX6 (also called SNX-BAR subcomplex); the respective CSC and SNX-BAR subcomplexes associate with low affinity. Interacts with SNX5, SNX6, SNX32, VPS26A, VPS29, VPS35, FNBP1, KALRN, RHOG (GDP-bound form).

Subcellular location. Early endosome membrane. Cell projection. Lamellipodium.

Domain organisation. The BAR domain is able to sense membrane curvature upon dimerization. Membrane remodeling seems to implicate insertion of a N-terminal amphipathic helix (AH) in the membrane.

Similarity. Belongs to the sorting nexin family.

Isoforms (2)

UniProt ID	Names	Canonical?
O60749-1	1	yes
O60749-2	2

RefSeq proteins (2): NP_001265128, NP_003091* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001683	PX_dom	Domain
IPR005329	Sorting_nexin_N	Domain
IPR015404	Vps5_C	Domain
IPR027267	AH/BAR_dom_sf	Homologous_superfamily
IPR036871	PX_dom_sf	Homologous_superfamily
IPR037918	SNX2_PX	Domain

Pfam: PF00787, PF03700, PF09325

UniProt features (29 total): modified residue 8, binding site 4, mutagenesis site 4, sequence conflict 4, region of interest 3, domain 2, compositionally biased region 2, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O60749-F1	76.87	0.56

Functional residue map

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

Ligand- & substrate-binding residues (4): 211; 235; 183; 185

Post-translational modifications (8): 97, 101, 104, 117, 119, 185, 277, 469

Mutagenesis-validated functional residues (4):

Position	Phenotype
182–184	decreases kalrn-dependent lamellipodium formation; no effect on interaction with kalrn.
211	abolishes phosphatidylinositol phosphate binding. abolishes endosomal location.
426	decreases kalrn-dependent lamellipodium formation; no effect on interaction with kalrn; when associated with a-428.
428	decreases kalrn-dependent lamellipodium formation; no effect on interaction with kalrn; when associated with a-426.

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-432722	Golgi Associated Vesicle Biogenesis
R-HSA-199991	Membrane Trafficking
R-HSA-199992	trans-Golgi Network Vesicle Budding
R-HSA-5653656	Vesicle-mediated transport

MSigDB gene sets: 0 (showing top):

GO Biological Process (5): intracellular protein transport (GO:0006886), early endosome to Golgi transport (GO:0034498), retrograde transport, endosome to Golgi (GO:0042147), lamellipodium morphogenesis (GO:0072673), protein transport (GO:0015031)

GO Molecular Function (11): epidermal growth factor receptor binding (GO:0005154), insulin receptor binding (GO:0005158), phosphatidylinositol binding (GO:0035091), identical protein binding (GO:0042802), protein homodimerization activity (GO:0042803), cadherin binding (GO:0045296), protein heterodimerization activity (GO:0046982), transferrin receptor binding (GO:1990459), leptin receptor binding (GO:1990460), protein binding (GO:0005515), lipid binding (GO:0008289)

GO Cellular Component (13): cytoplasm (GO:0005737), lysosome (GO:0005764), endosome (GO:0005768), cytosol (GO:0005829), endosome membrane (GO:0010008), membrane (GO:0016020), lamellipodium (GO:0030027), retromer complex (GO:0030904), retromer, tubulation complex (GO:0030905), early endosome membrane (GO:0031901), protein-containing complex (GO:0032991), cytoplasmic vesicle (GO:0031410), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
trans-Golgi Network Vesicle Budding	1
Vesicle-mediated transport	1
Membrane Trafficking	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
signaling receptor binding	3
intracellular protein localization	2
protein dimerization activity	2
binding	2
endomembrane system	2
cytoplasm	2
membrane protein complex	2
protein transport	1
intracellular transport	1
retrograde transport, endosome to Golgi	1
Golgi vesicle transport	1
intercellular transport	1
endosomal transport	1
cytosolic transport	1
lamellipodium organization	1
plasma membrane bounded cell projection morphogenesis	1
transport	1
establishment of protein localization	1
growth factor receptor binding	1
anion binding	1
protein binding	1
identical protein binding	1
cell adhesion molecule binding	1
intracellular anatomical structure	1
lytic vacuole	1
cytoplasmic vesicle	1
endosome	1
cytoplasmic vesicle membrane	1
bounding membrane of organelle	1
cell leading edge	1
plasma membrane bounded cell projection	1
retromer complex	1
early endosome	1
endosome membrane	1
cellular_component	1
intracellular vesicle	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

209 interactions, top by confidence:

A	B	Type	Score
SNX2	SNX6	psi-mi:“MI:0915”(physical association)	0.800
SNX6	SNX2	psi-mi:“MI:0914”(association)	0.800
SNX1	SNX2	psi-mi:“MI:0914”(association)	0.740
SNX32	SNX2	psi-mi:“MI:0914”(association)	0.740
SNX2	SNX32	psi-mi:“MI:0915”(physical association)	0.740
USP46	PHLPP1	psi-mi:“MI:0914”(association)	0.740
VAPB	FAM83G	psi-mi:“MI:0914”(association)	0.730
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
SNX2	FNBP1	psi-mi:“MI:0915”(physical association)	0.660
FNBP1	SNX2	psi-mi:“MI:0403”(colocalization)	0.660
FNBP1	SNX2	psi-mi:“MI:0915”(physical association)	0.660
VAPA	FAM83G	psi-mi:“MI:0914”(association)	0.640
IGF1R	PIK3R2	psi-mi:“MI:2364”(proximity)	0.590
SNX2	ARL6IP1	psi-mi:“MI:0915”(physical association)	0.560
SNX2	TMEM239	psi-mi:“MI:0915”(physical association)	0.560
SNX2	YIF1A	psi-mi:“MI:0915”(physical association)	0.560
SNX2	PNKP	psi-mi:“MI:0915”(physical association)	0.560
PLIN3	SNX2	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (312): SNX2 (Affinity Capture-MS), SNX2 (Affinity Capture-MS), SNX2 (Affinity Capture-MS), SNX2 (Affinity Capture-MS), SNX2 (Affinity Capture-MS), SNX2 (Affinity Capture-MS), SNX2 (Affinity Capture-MS), SNX2 (Affinity Capture-MS), SNX2 (Affinity Capture-MS), SNX2 (Affinity Capture-MS), SNX2 (Affinity Capture-MS), SNX2 (Affinity Capture-MS), CTPS1 (Co-fractionation), DDB1 (Co-fractionation), HGS (Co-fractionation)

ESM2 similar proteins: A0A098DRQ4, A1A4L0, A1CAN8, A1DF15, A1L1C7, A6RJQ7, A7E559, A7KAL4, B2AVN3, C8VDI2, C8VDQ4, I1RKA1, I1S4N7, O60749, O95219, P0C220, P83094, Q0WQF4, Q2TBW7, Q2U7R4, Q2UB56, Q4IR87, Q4WCV3, Q4WUE5, Q4WZF1, Q524W4, Q5AZC9, Q5R4C2, Q5R6M6, Q5R9A9, Q6NRZ4, Q6P3Q6, Q6PCS4, Q6VVX2, Q7SB54, Q7SB97, Q8J2R3, Q8K3H0, Q8VWF1, Q91VH2

Diamond homologs: B9DFS6, I1RXT2, O14243, O60493, O60749, O70492, O94291, P0C220, P0CR58, P0CR59, P0CR62, P0CR63, P47057, Q1RMH8, Q28E02, Q4I1H6, Q4R5U9, Q4V7P7, Q566W7, Q5R5V1, Q5R9A9, Q5U211, Q5VWJ9, Q7SH92, Q8CE50, Q8L5Z7, Q9CWK8, Q9CY18, Q9P779, Q9UNH6, A0A1B7YDZ4, O60107, O70493, P0CR60, P0CR61, Q08DD7, Q2TBW7, Q2U4K2, Q4P1V3, Q4PHC3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 150 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.

GO biological processes:

GO term	Partners	Fold	FDR
endoplasmic reticulum to Golgi vesicle-mediated transport	8	8.8×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	55
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2240 predictions. Top by Δscore:

Variant	Effect	Δscore
5:122775210:AGG:A	donor_loss	1.0000
5:122775211:GG:G	donor_loss	1.0000
5:122775212:GTGAG:G	donor_loss	1.0000
5:122775213:T:A	donor_loss	1.0000
5:122795261:A:AG	acceptor_gain	1.0000
5:122795262:A:G	acceptor_gain	1.0000
5:122795262:ACAGT:A	acceptor_loss	1.0000
5:122795263:CAG:C	acceptor_loss	1.0000
5:122795264:A:AG	acceptor_gain	1.0000
5:122795265:G:GA	acceptor_gain	1.0000
5:122795265:GT:G	acceptor_gain	1.0000
5:122795265:GTC:G	acceptor_gain	1.0000
5:122795265:GTCA:G	acceptor_gain	1.0000
5:122795265:GTCAA:G	acceptor_gain	1.0000
5:122795379:TGCAG:T	donor_loss	1.0000
5:122795380:GCAG:G	donor_gain	1.0000
5:122795380:GCAGG:G	donor_loss	1.0000
5:122795382:AGG:A	donor_loss	1.0000
5:122795383:GGTA:G	donor_loss	1.0000
5:122795384:G:GA	donor_loss	1.0000
5:122795385:T:A	donor_loss	1.0000
5:122799690:A:AG	acceptor_gain	1.0000
5:122799691:G:GG	acceptor_gain	1.0000
5:122799691:GAA:G	acceptor_gain	1.0000
5:122799813:GA:G	donor_gain	1.0000
5:122799815:G:GG	donor_gain	1.0000
5:122799850:G:T	donor_gain	1.0000
5:122799863:A:T	donor_gain	1.0000
5:122801860:A:AG	acceptor_gain	1.0000
5:122801861:C:G	acceptor_gain	1.0000

AlphaMissense

3435 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:122802098:T:G	Y159D	1.000
5:122802107:T:C	Y162H	1.000
5:122803515:G:C	R182T	1.000
5:122803515:G:T	R182I	1.000
5:122803516:A:C	R182S	1.000
5:122803516:A:T	R182S	1.000
5:122803517:A:G	R183G	1.000
5:122803518:G:C	R183T	1.000
5:122803518:G:T	R183I	1.000
5:122803519:A:C	R183S	1.000
5:122803519:A:T	R183S	1.000
5:122803520:T:C	F184L	1.000
5:122803521:T:C	F184S	1.000
5:122803521:T:G	F184C	1.000
5:122803522:C:A	F184L	1.000
5:122803522:C:G	F184L	1.000
5:122803527:A:G	D186G	1.000
5:122803527:A:T	D186V	1.000
5:122803539:T:C	L190S	1.000
5:122803574:G:C	G202R	1.000
5:122803575:G:A	G202D	1.000
5:122803596:C:A	P209Q	1.000
5:122803601:A:C	K211Q	1.000
5:122803603:G:C	K211N	1.000
5:122803603:G:T	K211N	1.000
5:122808291:A:G	K220E	1.000
5:122808293:A:C	K220N	1.000
5:122808293:A:T	K220N	1.000
5:122808324:T:C	F231L	1.000
5:122808325:T:G	F231C	1.000

dbSNP variants (sampled 300 via entrez): RS1000056889 (5:122834829 A>G), RS1000144450 (5:122775951 A>C), RS1000167897 (5:122784045 A>G), RS1000193567 (5:122834893 G>A,C), RS1000194016 (5:122792456 G>A,C), RS1000212823 (5:122825576 T>C), RS1000246351 (5:122832248 T>C,G), RS1000246566 (5:122781586 C>T), RS1000252050 (5:122798697 T>C,G), RS1000281545 (5:122798989 T>C), RS1000281803 (5:122786897 G>A,C), RS1000333930 (5:122789334 C>T), RS1000519365 (5:122833520 T>C), RS1000554193 (5:122815489 A>C), RS1000575872 (5:122791481 C>T)

Disease associations

OMIM: gene MIM:605929 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST003178_1	Event free survival in diffuse large B-cell lymphoma treated with immunochemotherapy	2.000000e-07
GCST010701_69	Cortical surface area (MOSTest)	2.000000e-09
GCST010702_176	Subcortical volume (MOSTest)	8.000000e-35
GCST010703_344	Brain morphology (MOSTest)	4.000000e-10
GCST90002400_648	Plateletcrit	2.000000e-31

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0000482	event free survival time
EFO:0007754	response to immunochemotherapy
EFO:0004346	neuroimaging measurement
EFO:0007985	platelet crit

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067023 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
10.00	Kd	0.1	nM	CHEMBL3752910
9.77	ED50	0.171	nM	CHEMBL3752910

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149941: Binding affinity to human SNX2 incubated for 45 mins by Kinobead based pull down assay	kd	0.0001	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases methylation, affects cotreatment, increases expression, affects expression	7
bisphenol A	decreases expression, increases expression	2
sodium arsenite	decreases expression, increases expression	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	2
bisphenol S	increases expression, affects cotreatment	2
Vorinostat	increases expression	2
Cadmium Chloride	increases abundance, decreases expression	2
FR900359	decreases phosphorylation	1
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
tetrahydropalmatine	decreases expression	1
arsenite	affects binding, increases reaction	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	affects binding, increases reaction	1
nutlin 3	increases secretion, affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
LDN 193189	affects cotreatment, increases expression	1
bisphenol AF	increases expression	1
Sunitinib	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Atrazine	increases expression	1
Benzo(a)pyrene	increases methylation	1
Cadmium	increases abundance, decreases expression	1
Caffeine	increases phosphorylation	1
Cisplatin	increases expression	1
Dactinomycin	affects cotreatment, increases expression, increases secretion	1
Dexamethasone	affects cotreatment, increases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652983	Binding	Binding affinity to human SNX2 incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B2GZ	Abcam HeLa SNX2 KO	Cancer cell line	Female

Clinical trials (associated diseases)

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