SNX32

Summary

SNX32 (sorting nexin 32, HGNC:26423) is a protein-coding gene on chromosome 11q13.1, encoding Sorting nexin-32 (Q86XE0). Involved in endosomal trafficking of cargo proteins, including transferrin-bound transferrin receptor (TFRC), cation-independent mannose-6-phosphate receptor (IGF2R) and epidermal growth factor receptor (EGFR).

Predicted to enable phosphatidylinositol binding activity. Predicted to be involved in retrograde transport, endosome to Golgi. Predicted to be located in cytoplasmic vesicle and cytosol. Predicted to be active in endosome.

Source: NCBI Gene 254122 — RefSeq curated summary.

At a glance

• GWAS associations: 12
• Clinical variants (ClinVar): 58 total
• MANE Select transcript: NM_152760

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26423
Approved symbol	SNX32
Name	sorting nexin 32
Location	11q13.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ30934
Ensembl gene	ENSG00000172803
Ensembl biotype	protein_coding
OMIM	621073
Entrez	254122

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 7 retained_intron, 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000308342, ENST00000524729, ENST00000526972, ENST00000530101, ENST00000531503, ENST00000531795, ENST00000533236, ENST00000533298, ENST00000534387, ENST00000913492, ENST00000946609, ENST00000946610

RefSeq mRNA: 1 — MANE Select: NM_152760 NM_152760

CCDS: CCDS8113

Canonical transcript exons

ENST00000308342 — 13 exons

Exon	Start	End
ENSE00001235659	65851328	65851403
ENSE00001235739	65853282	65853701
ENSE00002170734	65833963	65834101
ENSE00002501828	65851640	65851679
ENSE00003494926	65850150	65850271
ENSE00003513049	65850751	65850855
ENSE00003530657	65849478	65849582
ENSE00003575550	65850431	65850554
ENSE00003587068	65849920	65850030
ENSE00003612000	65852630	65852789
ENSE00003649426	65852465	65852551
ENSE00003657800	65851055	65851160
ENSE00003674961	65852873	65852958

Expression profiles

Bgee: expression breadth ubiquitous, 163 present calls, max score 93.56.

FANTOM5 (CAGE): breadth broad, TPM avg 1.9727 / max 143.5361, expressed in 609 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
115214	1.4526	524
115215	0.5201	193

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right frontal lobe	UBERON:0002810	93.56	gold quality
Brodmann (1909) area 9	UBERON:0013540	91.58	gold quality
nucleus accumbens	UBERON:0001882	90.99	gold quality
caudate nucleus	UBERON:0001873	90.31	gold quality
anterior cingulate cortex	UBERON:0009835	90.30	gold quality
putamen	UBERON:0001874	89.52	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	88.64	gold quality
prefrontal cortex	UBERON:0000451	87.20	gold quality
cortical plate	UBERON:0005343	86.77	gold quality
amygdala	UBERON:0001876	86.63	gold quality
neocortex	UBERON:0001950	86.50	gold quality
frontal cortex	UBERON:0001870	86.11	gold quality
right hemisphere of cerebellum	UBERON:0014890	86.01	gold quality
cerebellar hemisphere	UBERON:0002245	84.71	gold quality
cerebral cortex	UBERON:0000956	84.51	gold quality
cerebellar cortex	UBERON:0002129	84.49	gold quality
cerebellum	UBERON:0002037	82.83	gold quality
hypothalamus	UBERON:0001898	82.55	gold quality
forebrain	UBERON:0001890	82.47	gold quality
primary visual cortex	UBERON:0002436	82.06	gold quality
brain	UBERON:0000955	81.72	gold quality
Ammon’s horn	UBERON:0001954	81.41	gold quality
temporal lobe	UBERON:0001871	79.47	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	77.79	gold quality
sperm	CL:0000019	77.71	silver quality
occipital lobe	UBERON:0002021	76.55	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	76.40	gold quality
ganglionic eminence	UBERON:0004023	75.15	gold quality
superior frontal gyrus	UBERON:0002661	74.92	gold quality
substantia nigra	UBERON:0002038	74.57	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-CURD-112	yes	15172.68
E-MTAB-9543	yes	3567.33
E-ANND-3	yes	18.96
E-MTAB-8060	no	81.20

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NR1I2

miRNA regulators (miRDB)

25 targeting SNX32, 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-4455	100.00	65.48	1587
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-187-5P	99.74	70.26	1404
HSA-MIR-670-5P	99.67	69.94	1565
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-125A-5P	99.36	70.59	1640
HSA-MIR-125B-5P	99.36	70.36	1662
HSA-MIR-145-3P	99.33	67.66	764
HSA-MIR-6852-5P	99.17	66.69	2073
HSA-MIR-876-3P	98.76	68.23	945
HSA-MIR-323A-5P	98.59	65.13	651
HSA-MIR-6804-5P	98.39	65.77	1084
HSA-MIR-1262	98.17	66.52	757
HSA-MIR-3127-5P	97.52	65.24	786
HSA-MIR-3918	96.13	64.65	1300
HSA-MIR-4435	95.90	65.47	1201
HSA-MIR-4683	95.29	65.98	631
HSA-MIR-6732-5P	93.97	64.65	422
HSA-MIR-450A-5P	93.89	64.57	50

Literature-anchored findings (GeneRIF, showing 1)

• SNX32 Regulates Sorting and Trafficking of Activated EGFR to the Lysosomal Degradation Pathway. (PMID:39073202)

Cross-species orthologs

9 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:dkey-28n18.9	ENSDARG00000097193
mus_musculus	Snx32	ENSMUSG00000056185
rattus_norvegicus	Snx32	ENSRNOG00000026527
drosophila_melanogaster	Snx1	FBGN0031534
drosophila_melanogaster	Snx6	FBGN0032005
drosophila_melanogaster	SH3PX1	FBGN0040475
caenorhabditis_elegans		WBGENE00003086
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), SNX33 (ENSG00000173548), SNX18 (ENSG00000178996), SNX2 (ENSG00000205302)

Protein

Protein identifiers

Sorting nexin-32 — Q86XE0 (reviewed: Q86XE0)

Alternative names: Sorting nexin-6B

All UniProt accessions (1): Q86XE0

UniProt curated annotations — full annotation on UniProt →

Function. Involved in endosomal trafficking of cargo proteins, including transferrin-bound transferrin receptor (TFRC), cation-independent mannose-6-phosphate receptor (IGF2R) and epidermal growth factor receptor (EGFR). Functions redundantly with other BAR domain-containing sorting nexins in endosome to trans-Golgi network transport of IGF2R. Regulates in coordination with SNX5 sorting and trafficking of EGF-activated EGFR to multivesicular bodies for lysosomal degradation. Plays an essential role in neurite outgrowth, controlling basigin/EMMPRIN (BSG) trafficking to the cell surface.

Subunit / interactions. Interacts with BAR domain-containing sorting nexins SNX1, SNX2, SNX4, SNX5 and SNX6. Interacts (via PX domain) with cargo proteins transferrin-bound TFRC, IGF2R and BSG; the interaction regulates their intracellular trafficking. Interacts with EGFR; the interaction is required for endolysosomal EGFR trafficking.

Subcellular location. Cell membrane. Early endosome. Golgi apparatus. trans-Golgi network. Recycling endosome. Late endosome.

Similarity. Belongs to the sorting nexin family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q86XE0-1	1	yes
Q86XE0-2	2

RefSeq proteins (1): NP_689973* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001683	PX_dom	Domain
IPR014637	SNX5/SNX6/SNX32	Family
IPR015404	Vps5_C	Domain
IPR027267	AH/BAR_dom_sf	Homologous_superfamily
IPR036871	PX_dom_sf	Homologous_superfamily

Pfam: PF00787, PF09325

UniProt features (20 total): helix 6, strand 3, sequence variant 3, splice variant 2, mutagenesis site 2, chain 1, domain 1, sequence conflict 1, coiled-coil region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
6E8R	X-RAY DIFFRACTION	2.27

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86XE0-F1	89.43	0.72

Functional residue map

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

Mutagenesis-validated functional residues (2):

Position	Phenotype
131	loss of interaction with tfrc, igf2r and bsg. does not affect interaction with snx1.
256	decreased interaction with snx5.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 95 (showing top): GOBP_REGULATION_OF_AUTOPHAGY, GOBP_LYSOSOMAL_TRANSPORT, GOBP_ENDOSOME_ORGANIZATION, GOBP_NEURON_PROJECTION_EXTENSION, GOBP_VESICLE_ORGANIZATION, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOBP_ENDOSOME_TO_LYSOSOME_TRANSPORT, GOBP_GROWTH, GOBP_VACUOLAR_TRANSPORT, GOBP_NEUROGENESIS, GOBP_VESICLE_MEDIATED_TRANSPORT, chr11q13, GOBP_MACROAUTOPHAGY, GOCC_TRANS_GOLGI_NETWORK, GOBP_REGULATION_OF_CATABOLIC_PROCESS

GO Biological Process (6): protein transport (GO:0015031), endosomal transport (GO:0016197), regulation of macroautophagy (GO:0016241), endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510), retrograde transport, endosome to Golgi (GO:0042147), neuron projection extension (GO:1990138)

GO Molecular Function (3): dynactin binding (GO:0034452), phosphatidylinositol binding (GO:0035091), protein binding (GO:0005515)

GO Cellular Component (10): endosome (GO:0005768), early endosome (GO:0005769), late endosome (GO:0005770), trans-Golgi network (GO:0005802), cytosol (GO:0005829), plasma membrane (GO:0005886), retromer complex (GO:0030904), early endosome membrane (GO:0031901), recycling endosome (GO:0055037), tubular endosome (GO:0097422)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
endosome	4
endomembrane system	2
cellular anatomical structure	2
transport	1
intracellular protein localization	1
establishment of protein localization	1
vesicle-mediated transport	1
intracellular transport	1
regulation of autophagy	1
macroautophagy	1
endosome to lysosome transport	1
endosome transport via multivesicular body sorting pathway	1
intercellular transport	1
endosomal transport	1
cytosolic transport	1
developmental cell growth	1
neuron projection morphogenesis	1
developmental growth involved in morphogenesis	1
cytoskeletal protein binding	1
anion binding	1
binding	1
cytoplasmic vesicle	1
Golgi apparatus subcompartment	1
cytoplasm	1
membrane	1
cell periphery	1
membrane protein complex	1
early endosome	1
endosome membrane	1

Protein interactions and networks

STRING

660 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SNX32	SNX2	P82862	980
SNX32	SNX1	Q13596	965
SNX32	SNX5	Q9Y5X3	800
SNX32	SNX6	Q9UNH7	712
SNX32	SNX7	Q9UNH6	668
SNX32	VPS29	Q9UBQ0	658
SNX32	SNX8	Q9Y5X2	643
SNX32	SNX33	Q8WV41	637
SNX32	VPS26A	O75436	633
SNX32	SNX27	Q96L92	620
SNX32	VPS35	Q96QK1	599
SNX32	VPS26B	Q4G0F5	598
SNX32	SNX3	O60493	584
SNX32	SNX18	Q96RF0	571
SNX32	SNX4	O95219	568

IntAct

44 interactions, top by confidence:

A	B	Type	Score
SNX1	SNX32	psi-mi:“MI:0915”(physical association)	0.870
SNX32	SNX2	psi-mi:“MI:0914”(association)	0.740
SNX2	SNX32	psi-mi:“MI:0915”(physical association)	0.740
SNX1	SNX2	psi-mi:“MI:0914”(association)	0.740
SNX32	TFIP11	psi-mi:“MI:0915”(physical association)	0.560
SNX32	NME7	psi-mi:“MI:0915”(physical association)	0.560
SNX32	SPANXB1	psi-mi:“MI:0915”(physical association)	0.560
GRXCR1	SNX32	psi-mi:“MI:0915”(physical association)	0.560
EML2	SNX32	psi-mi:“MI:0915”(physical association)	0.560
SNX32	MNS1	psi-mi:“MI:0915”(physical association)	0.560
C22orf39	SNX32	psi-mi:“MI:0915”(physical association)	0.560
incE	SNX2	psi-mi:“MI:0914”(association)	0.430
SNX30	SNX32	psi-mi:“MI:0915”(physical association)	0.400
M		psi-mi:“MI:0914”(association)	0.350
SNX32	CHMP2A	psi-mi:“MI:0914”(association)	0.350
SNX32	SNX2	psi-mi:“MI:0915”(physical association)	0.000
SNX32	SNX1	psi-mi:“MI:0915”(physical association)	0.000
SNX32	TFIP11	psi-mi:“MI:0915”(physical association)	0.000
SNX1	SNX32	psi-mi:“MI:0915”(physical association)	0.000
NME7	SNX32	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (38): SNX32 (Two-hybrid), SNX1 (Two-hybrid), SNX1 (Affinity Capture-MS), SNX6 (Affinity Capture-MS), RAD51 (Affinity Capture-MS), IFFO1 (Affinity Capture-MS), SNX2 (Affinity Capture-MS), CEP44 (Affinity Capture-MS), RNF40 (Affinity Capture-MS), BRCA2 (Affinity Capture-MS), PIK3R1 (Affinity Capture-MS), TEX11 (Two-hybrid), TSG101 (Two-hybrid), SNX32 (Two-hybrid), SNX32 (Two-hybrid)

ESM2 similar proteins: A0A1B7YDZ4, B1H267, I1RXT2, O14243, O60107, O74960, O94447, P0CR58, P0CR59, P0CR62, P0CR63, P0CR64, P0CR65, P32912, P32913, P40531, P40959, P47057, Q09746, Q10253, Q28GP7, Q3ZBM5, Q4PHC3, Q4VAA7, Q4WQI6, Q522W5, Q5B797, Q5R613, Q6C238, Q6C9X0, Q6CGJ5, Q6CHY6, Q6CTQ0, Q6CUC4, Q6FPT9, Q6NRL2, Q6P8X1, Q759T1, Q75B65, Q75C43

Diamond homologs: B1H267, Q3ZBM5, Q4V7P7, Q5R613, Q6P8X1, Q80ZJ7, Q86XE0, Q9D8U8, Q9UNH7, Q9Y5X3, B9DFS6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	51
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2581 predictions. Top by Δscore:

Variant	Effect	Δscore
11:65850010:GAGGA:G	donor_gain	1.0000
11:65850012:G:GT	donor_gain	1.0000
11:65850012:GGA:G	donor_gain	1.0000
11:65850013:G:GT	donor_gain	1.0000
11:65850013:GA:G	donor_gain	1.0000
11:65850015:G:GG	donor_gain	1.0000
11:65850031:G:GG	donor_gain	1.0000
11:65850036:G:GT	donor_gain	1.0000
11:65850270:GC:G	donor_gain	1.0000
11:65850272:G:GG	donor_gain	1.0000
11:65850430:GGGA:G	acceptor_gain	1.0000
11:65850551:GGAT:G	donor_gain	1.0000
11:65850552:G:GT	donor_gain	1.0000
11:65850560:C:G	donor_gain	1.0000
11:65850741:T:TA	acceptor_gain	1.0000
11:65850750:GCT:G	acceptor_gain	1.0000
11:65851159:GT:G	donor_gain	1.0000
11:65851161:G:GG	donor_gain	1.0000
11:65851396:C:G	donor_gain	1.0000
11:65851404:G:GG	donor_gain	1.0000
11:65852443:A:AG	acceptor_gain	1.0000
11:65852444:G:GG	acceptor_gain	1.0000
11:65852624:TCCTA:T	acceptor_loss	1.0000
11:65852625:CCTAG:C	acceptor_loss	1.0000
11:65852626:CTAG:C	acceptor_loss	1.0000
11:65852627:TAGG:T	acceptor_loss	1.0000
11:65852628:A:AG	acceptor_gain	1.0000
11:65852628:A:T	acceptor_loss	1.0000
11:65852629:G:GG	acceptor_gain	1.0000
11:65852629:G:T	acceptor_loss	1.0000

AlphaMissense

2630 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:65849565:T:C	F42L	1.000
11:65849567:C:A	F42L	1.000
11:65849567:C:G	F42L	1.000
11:65849572:T:A	V44D	1.000
11:65850447:T:C	F131L	1.000
11:65850449:T:A	F131L	1.000
11:65850449:T:G	F131L	1.000
11:65849566:T:C	F42S	0.999
11:65849977:T:C	F67L	0.999
11:65849978:T:C	F67S	0.999
11:65849979:C:A	F67L	0.999
11:65849979:C:G	F67L	0.999
11:65849987:T:C	L70P	0.999
11:65850163:C:A	P89H	0.999
11:65850177:T:C	F94L	0.999
11:65850179:T:A	F94L	0.999
11:65850179:T:G	F94L	0.999
11:65850257:G:C	K120N	0.999
11:65850257:G:T	K120N	0.999
11:65850435:T:C	Y127H	0.999
11:65850436:A:G	Y127C	0.999
11:65850439:T:C	L128P	0.999
11:65850448:T:C	F131S	0.999
11:65850452:G:C	K132N	0.999
11:65850452:G:T	K132N	0.999
11:65850460:T:A	V135D	0.999
11:65850534:T:C	F160L	0.999
11:65850536:T:A	F160L	0.999
11:65850536:T:G	F160L	0.999
11:65852499:T:C	L287P	0.999

dbSNP variants (sampled 300 via entrez): RS1000042091 (11:65850810 G>A,C), RS1000181791 (11:65834582 T>G), RS1000239290 (11:65839629 C>G), RS1000311415 (11:65839329 A>C), RS1000519348 (11:65833146 G>A,T), RS1000585621 (11:65840103 C>T), RS1000594143 (11:65834189 CTGTG>C,CTG,CTGTGTG,CTGTGTGTG), RS1000645432 (11:65840750 G>A), RS1000660508 (11:65832718 C>T), RS1000823349 (11:65833454 G>A), RS1000918035 (11:65834382 T>G), RS1000956254 (11:65840402 G>A,T), RS1001019694 (11:65848003 G>A), RS1001046107 (11:65847530 C>T), RS1001194170 (11:65839666 AT>A)

Disease associations

OMIM: gene MIM:621073 | 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
GCST001725_13	Inflammatory bowel disease	3.000000e-10
GCST001937_15	Breast cancer	9.000000e-12
GCST002481_8	Acne (severe)	3.000000e-11
GCST005790_23	Rosacea symptom severity	1.000000e-08
GCST006408_13	Allergic sensitization	3.000000e-07
GCST008362_125	Birth weight	2.000000e-08
GCST90002398_198	Neutrophil count	4.000000e-12
GCST90002402_353	Platelet count	2.000000e-10
GCST90002407_330	White blood cell count	7.000000e-18
GCST90020025_1881	Waist-to-hip ratio adjusted for BMI	7.000000e-12
GCST90020027_1497	Waist-hip index	4.000000e-12
GCST90020029_331	Waist circumference adjusted for body mass index	2.000000e-11

EFO canonical traits (7, from GWAS)

EFO ID	Trait name
EFO:0009180	rosacea severity measurement
EFO:0005298	allergic sensitization measurement
EFO:0004344	birth weight
EFO:0004833	neutrophil count
EFO:0004309	platelet count
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0007789	BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol S	decreases expression, decreases methylation	2
aristolochic acid I	increases expression	1
GSK-J4	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	decreases expression	1
sodium arsenite	decreases expression	1
Acetaminophen	decreases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases methylation	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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