SNX31

gene
On this page

Also known as MGC39715

Summary

SNX31 (sorting nexin 31, HGNC:28605) is a protein-coding gene on chromosome 8q22.3, encoding Sorting nexin-31 (Q8N9S9). May be involved in protein trafficking.

Predicted to enable phosphatidylinositol binding activity. Predicted to be involved in endocytic recycling and intracellular protein transport. Predicted to be located in cytoskeleton. Predicted to be part of protein-containing complex. Predicted to be active in early endosome.

Source: NCBI Gene 169166 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): schizophrenia (No Known Disease Relationship, GenCC)
  • GWAS associations: 11
  • Clinical variants (ClinVar): 92 total
  • MANE Select transcript: NM_152628

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28605
Approved symbolSNX31
Namesorting nexin 31
Location8q22.3
Locus typegene with protein product
StatusApproved
AliasesMGC39715
Ensembl geneENSG00000174226
Ensembl biotypeprotein_coding
OMIM619839
Entrez169166

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 10 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000311812, ENST00000428383, ENST00000518342, ENST00000519521, ENST00000520352, ENST00000520661, ENST00000520743, ENST00000862895, ENST00000862896, ENST00000960793, ENST00000960794

RefSeq mRNA: 2 — MANE Select: NM_152628 NM_001363720, NM_152628

CCDS: CCDS6288, CCDS87622

Canonical transcript exons

ENST00000311812 — 14 exons

ExonStartEnd
ENSE00001193755100596639100596842
ENSE00001193759100600349100600441
ENSE00001193765100608494100608563
ENSE00001193767100612000100612087
ENSE00001193773100612995100613085
ENSE00001193777100617620100617730
ENSE00001193787100649274100649348
ENSE00001265091100630327100630391
ENSE00001265110100577019100577075
ENSE00001265163100572889100573960
ENSE00001265171100649449100649665
ENSE00003473139100584111100584188
ENSE00003487029100635897100636011
ENSE00003667642100588866100588979

Expression profiles

Bgee: expression breadth ubiquitous, 163 present calls, max score 92.00.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0845 / max 19.2337, expressed in 30 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
941530.038915
941540.031114
941520.01456

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099192.00gold quality
buccal mucosa cellCL:000233688.57silver quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047388.52gold quality
oral cavityUBERON:000016782.78gold quality
urinary bladderUBERON:000125581.22gold quality
epithelium of nasopharynxUBERON:000195178.87silver quality
endothelial cellCL:000011578.54silver quality
esophagus squamous epitheliumUBERON:000692076.05gold quality
lower esophagus mucosaUBERON:003583475.31gold quality
spermCL:000001974.40silver quality
esophagus mucosaUBERON:000246973.94gold quality
pharyngeal mucosaUBERON:000035571.86gold quality
olfactory segment of nasal mucosaUBERON:000538667.84gold quality
tonsilUBERON:000237267.44gold quality
palpebral conjunctivaUBERON:000181264.77silver quality
esophagusUBERON:000104364.58gold quality
left testisUBERON:000453364.26gold quality
right testisUBERON:000453463.75gold quality
testisUBERON:000047363.37gold quality
urethraUBERON:000005762.43silver quality
mucosa of stomachUBERON:000119962.20gold quality
vaginaUBERON:000099660.89gold quality
ventricular zoneUBERON:000305360.63gold quality
prostate glandUBERON:000236759.60gold quality
mucosa of paranasal sinusUBERON:000503059.52gold quality
smooth muscle tissueUBERON:000113559.48gold quality
bronchial epithelial cellCL:000232858.44silver quality
bronchusUBERON:000218557.82silver quality
cerebellar vermisUBERON:000472057.52gold quality
heart left ventricleUBERON:000208456.88gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

71 targeting SNX31, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3163100.0077.238605
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-548AW99.9972.573559
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-569699.9872.364487
HSA-MIR-9-3P99.9670.882068
HSA-MIR-651-3P99.9473.485177
HSA-MIR-454-3P99.9174.011925
HSA-MIR-130A-3P99.9073.311861
HSA-MIR-130B-3P99.9073.271850
HSA-MIR-301A-3P99.9073.151839
HSA-MIR-301B-3P99.9073.191836
HSA-MIR-366699.9073.241833
HSA-MIR-429599.9073.111838
HSA-MIR-548D-3P99.8770.674362
HSA-MIR-548BB-3P99.8670.584354
HSA-MIR-369-3P99.8570.522264
HSA-MIR-576-5P99.8470.462582
HSA-MIR-548AC99.8470.774351
HSA-MIR-548H-3P99.8470.804349
HSA-MIR-548Z99.8470.804349
HSA-MIR-449599.8272.083080
HSA-MIR-3121-3P99.8271.963630
HSA-MIR-442099.8270.081624
HSA-MIR-181B-2-3P99.8170.061646
HSA-MIR-181B-3P99.8170.061646
HSA-MIR-3059-5P99.7069.932491
HSA-MIR-472999.6972.184233
HSA-MIR-128499.6773.561353

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusSnx31ENSMUSG00000013611
rattus_norvegicusSnx31ENSRNOG00000025501

Paralogs (2): SNX17 (ENSG00000115234), SNX27 (ENSG00000143376)

Protein

Protein identifiers

Sorting nexin-31Q8N9S9 (reviewed: Q8N9S9)

All UniProt accessions (5): Q8N9S9, E5RFI8, E5RJE9, E5RJK2, H0YBA9

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in protein trafficking.

Subunit / interactions. Interacts with CCDC22, CCDC93, VPS26C and VPS35L, associates with the retriever and CCC complexes.

Similarity. Belongs to the sorting nexin family.

Isoforms (2)

UniProt IDNamesCanonical?
Q8N9S9-11yes
Q8N9S9-22

RefSeq proteins (2): NP_001350649, NP_689841* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001683PX_domDomain
IPR011993PH-like_dom_sfHomologous_superfamily
IPR036871PX_dom_sfHomologous_superfamily
IPR040842SNX17/31_FERMDomain
IPR048763SNX17-31_FERM_F1Domain
IPR048767SNX17-31_FERM_F2Domain

Pfam: PF00787, PF18116, PF21271, PF21273

UniProt features (10 total): sequence variant 3, splice variant 2, sequence conflict 2, chain 1, domain 1, mutagenesis site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N9S9-F184.770.68

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 (1):

PositionPhenotype
440strongly decreases interaction with ccdc22, ccdc93, vps26c and vps35l.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 68 (showing top): GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_VESICLE_MEDIATED_TRANSPORT, NIKOLSKY_BREAST_CANCER_8Q12_Q22_AMPLICON, chr8q22, GOBP_ENDOCYTIC_RECYCLING, GOBP_LOCALIZATION_WITHIN_MEMBRANE, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, GOMF_PHOSPHATIDYLINOSITOL_BINDING, GOMF_LIPID_BINDING, GOMF_PHOSPHOLIPID_BINDING, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MIKKELSEN_ES_ICP_WITH_H3K4ME3, GOBP_ENDOSOMAL_TRANSPORT, GOBP_INTRACELLULAR_TRANSPORT, GOBP_VESICLE_MEDIATED_TRANSPORT_TO_THE_PLASMA_MEMBRANE

GO Biological Process (3): intracellular protein transport (GO:0006886), endocytic recycling (GO:0032456), protein transport (GO:0015031)

GO Molecular Function (2): phosphatidylinositol binding (GO:0035091), protein binding (GO:0005515)

GO Cellular Component (3): early endosome (GO:0005769), protein-containing complex (GO:0032991), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
intracellular protein localization2
protein transport1
intracellular transport1
endosomal transport1
vesicle-mediated transport to the plasma membrane1
transport1
establishment of protein localization1
anion binding1
binding1
endosome1
cellular_component1
intracellular membraneless organelle1

Protein interactions and networks

STRING

386 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SNX31WHR1P49842697
SNX31TACC1O75410667
SNX31VPS26CO14972628
SNX31PPP6CO00743612
SNX31VPS29Q9UBQ0593
SNX31RDXP35241541
SNX31VPS35LQ7Z3J2539
SNX31ARID2Q68CP9519
SNX31MSNP26038517
SNX31EZRP15311502
SNX31HRASP01112475
SNX31SNX8Q9Y5X2456
SNX31SNX3O60493452
SNX31SNX1Q13596443
SNX31DGKZQ13574440

IntAct

7 interactions, top by confidence:

ABTypeScore
SNX31LZTS2psi-mi:“MI:0915”(physical association)0.560
LZTS2SNX31psi-mi:“MI:0915”(physical association)0.560
SNX31ATP5F1Apsi-mi:“MI:0915”(physical association)0.400
NUDCD2SNX31psi-mi:“MI:0915”(physical association)0.400
TRIM69POTEFpsi-mi:“MI:0914”(association)0.350

BioGRID (7): SNX31 (Two-hybrid), SNX31 (Two-hybrid), SNX31 (Affinity Capture-MS), SNX31 (Two-hybrid), SNX31 (Two-hybrid), SNX31 (Proximity Label-MS), SNX31 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GW35, A6QNM3, B0R034, B1ANS9, B9EK06, D2KC46, D3ZY60, F1MS15, F1P065, F1REV3, O00522, O15091, O75747, P10911, P58069, Q008S8, Q14449, Q14D04, Q15283, Q32NR9, Q45GW3, Q4R366, Q4R6T7, Q5H9U9, Q5K651, Q5PQS3, Q5XGX5, Q5XIZ9, Q5ZLD2, Q60862, Q63713, Q69Z37, Q6DCF6, Q6S5J6, Q6TNJ1, Q75PQ8, Q80W71, Q86VD1, Q86YR7, Q8C5W4

Diamond homologs: A5DHC9, Q5AG56, Q6BIS2, Q6FR40, Q6P8Y7, Q8N9S9, Q15036, Q28HD5, Q5EA77, Q5R4A5, Q5RID7, Q6AYS6, Q6DDY6, Q8BVL3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance73
Likely benign8
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3545 predictions. Top by Δscore:

VariantEffectΔscore
8:100612621:T:TAdonor_gain1.0000
8:100612627:A:Cdonor_gain1.0000
8:100613093:C:CTacceptor_gain1.0000
8:100613094:A:Tacceptor_gain1.0000
8:100615201:T:TCacceptor_gain1.0000
8:100617613:AGCTT:Adonor_loss1.0000
8:100617614:GCTT:Gdonor_loss1.0000
8:100617615:CTTA:Cdonor_loss1.0000
8:100617616:TTA:Tdonor_loss1.0000
8:100617617:TA:Tdonor_loss1.0000
8:100617618:A:ATdonor_loss1.0000
8:100621816:T:TAdonor_gain1.0000
8:100649454:AGCGG:Adonor_gain1.0000
8:100649455:G:Cdonor_gain1.0000
8:100573958:CTG:Cacceptor_gain0.9900
8:100573961:C:CCacceptor_gain0.9900
8:100577014:CAGA:Cdonor_gain0.9900
8:100596662:TC:Tdonor_gain0.9900
8:100596860:A:Cacceptor_gain0.9900
8:100600309:C:CAdonor_gain0.9900
8:100612085:CAA:Cacceptor_gain0.9900
8:100612088:C:CCacceptor_gain0.9900
8:100612600:A:ACdonor_gain0.9900
8:100612617:ATATT:Adonor_gain0.9900
8:100612656:T:TAdonor_gain0.9900
8:100612985:T:TAdonor_gain0.9900
8:100617618:A:ACdonor_gain0.9900
8:100617619:C:CCdonor_gain0.9900
8:100617619:CCT:Cdonor_gain0.9900
8:100617726:GTATT:Gacceptor_gain0.9900

AlphaMissense

2924 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
8:100635928:C:AR75S0.991
8:100635928:C:GR75S0.991
8:100635929:C:GR75T0.982
8:100649285:A:GW44R0.982
8:100649285:A:TW44R0.982
8:100636010:A:GL48P0.979
8:100635976:G:CF59L0.978
8:100635976:G:TF59L0.978
8:100635978:A:GF59L0.978
8:100649303:A:CY38D0.978
8:100613029:A:CF163L0.975
8:100613029:A:TF163L0.975
8:100613031:A:GF163L0.975
8:100649293:A:GL41P0.975
8:100635929:C:AR75M0.974
8:100635917:A:GL79P0.972
8:100635905:A:GL83S0.970
8:100635909:A:CY82D0.968
8:100635977:A:GF59S0.968
8:100649303:A:GY38H0.968
8:100649302:T:GY38S0.966
8:100635967:C:AK62N0.965
8:100635967:C:GK62N0.965
8:100649306:G:TR37S0.965
8:100649495:A:GI7T0.964
8:100635917:A:TL79Q0.960
8:100649284:C:GW44S0.960
8:100649303:A:TY38N0.957
8:100630345:A:CF101L0.956
8:100630345:A:TF101L0.956

dbSNP variants (sampled 300 via entrez): RS1000008949 (8:100581937 C>T), RS1000098090 (8:100651877 G>A), RS1000116299 (8:100616424 T>C), RS1000234429 (8:100616182 G>A), RS1000285701 (8:100574798 G>A), RS1000301320 (8:100627063 C>T), RS1000315032 (8:100654344 C>T), RS1000326217 (8:100651443 G>A,C), RS1000354033 (8:100627354 AAAAC>A,AAAACAAAC,AAAACAAACAAAC), RS1000423953 (8:100659953 A>C), RS1000451440 (8:100609553 A>G), RS1000465040 (8:100579837 T>C), RS1000472116 (8:100610392 T>C), RS1000482341 (8:100639399 G>A), RS1000485793 (8:100591054 CAA>C)

Disease associations

OMIM: gene MIM:619839 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
schizophreniaNo Known Disease RelationshipUnknown

Mondo (1): schizophrenia (MONDO:0005090)

Orphanet (0):

HPO phenotypes

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

GWAS associations

11 associations (top):

StudyTraitp-value
GCST003134_9Cerebrospinal fluid clusterin levels3.000000e-06
GCST004280_31Diastolic blood pressure2.000000e-09
GCST005714_1Cerebrospinal fluid beta-site APP cleaving enzyme levels3.000000e-06
GCST005951_63Body mass index2.000000e-08
GCST008155_29Waist-hip ratio9.000000e-06
GCST009391_2108Metabolite levels2.000000e-07
GCST009391_415Metabolite levels7.000000e-06
GCST010703_117Brain morphology (MOSTest)3.000000e-18
GCST010726_36Periventricular white matter hyperintensities2.000000e-06
GCST011743_48HDL cholesterol levels in HIV infection9.000000e-06
GCST011973_1Colorectal cancer2.000000e-06

EFO canonical traits (9, from GWAS)

EFO IDTrait name
EFO:0006336diastolic blood pressure
EFO:0009179beta-secretase 1 measurement
EFO:0004340body mass index
EFO:0004343waist-hip ratio
EFO:0010381phosphatidylcholine 36:3 measurement
EFO:0010387phosphatidylcholine 38:5 measurement
EFO:0004346neuroimaging measurement
EFO:0005665white matter hyperintensity measurement
EFO:0004612high density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

ChemicalActions (top 5)PubMed papers
Cadmium Chlorideincreases abundance, decreases expression2
bisphenol Aaffects cotreatment, decreases methylation1
sodium arseniteincreases expression1
butyraldehydeincreases expression1
benzo(e)pyreneincreases methylation1
aflatoxin B2increases methylation1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression1
Fulvestrantaffects cotreatment, decreases methylation1
Benzo(a)pyrenedecreases methylation1
Cadmiumdecreases expression, increases abundance1
Lipopolysaccharidesaffects response to substance, increases expression1
Methapyrileneincreases methylation1
Silicon Dioxideaffects expression1
Tobacco Smoke Pollutiondecreases expression1
Valproic Acidincreases methylation1
Aflatoxin B1increases methylation1
Antirheumatic Agentsdecreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00000374PHASE4COMPLETEDTreatment for First-Episode Schizophrenia
NCT00001656PHASE4COMPLETEDComparison of Clozapine vs Olanzapine in Childhood-Onset Psychotic Disorders
NCT00007774PHASE4COMPLETEDTo Determine if Olanzapine is More Cost Effective Than Haloperidol for the Treatment of Schizophrenia
NCT00014001PHASE4COMPLETEDCATIE- Schizophrenia Trial
NCT00018668PHASE4COMPLETEDAntipsychotic Response in Schizophrenia
NCT00034801PHASE4COMPLETEDOlanzapine Versus Active Comparator in the Treatment of Depression in Patients With Schizophrenia
NCT00034905PHASE4COMPLETEDA Comparison of Seroquel vs. Risperidone in Schizophrenia
NCT00036088PHASE4COMPLETEDOlanzapine Versus An Active Comparator in the Treatment of Schizophrenia
NCT00044187PHASE4COMPLETEDThe Assessment of a Weight-Gain Agent for the Treatment of Olanzapine-Associated Anti-Obesity Agent in Patients With Schizophrenia, Schizophreniform Disorder, Schizoaffective Disorder, and Bipolar I Disorder
NCT00044655PHASE4COMPLETEDSwitching Medication to Treat Schizophrenia
NCT00048828PHASE4COMPLETEDTreating Drug-Resistant Childhood Schizophrenia
NCT00053703PHASE4COMPLETEDTreatment of Early Onset Schizophrenia Spectrum Disorders (TEOSS)
NCT00056498PHASE4COMPLETEDRisperidone Treatment in Schizophrenia Patients Who Are Currently Taking Clozapine
NCT00061802PHASE4COMPLETEDEfficacy and Safety of Two Atypical Antipsychotics vs. Placebo in Patients With an Acute Exacerbation of Either Schizophrenia or Schizoaffective Disorder
NCT00080327PHASE4COMPLETEDStudy of Three Doses of Aripiprazole in Patients With Acute Schizophrenia
NCT00088049PHASE4COMPLETEDStudy of Olanzapine vs. Aripiprazole in the Treatment of Schizophrenia
NCT00090012PHASE4COMPLETEDComparison of Continuing Olanzapine to Switching to Quetiapine in Overweight or Obese Patients With Schizophrenia and Schizoaffective Disorder
NCT00100776PHASE4COMPLETEDEfficacy of High Dose Olanzapine for the Treatment of Schizophrenia and Schizoaffective Disorder
NCT00103571PHASE4COMPLETEDOlanzapine Versus Aripiprazole in the Treatment of Acutely Ill Patients With Schizophrenia
NCT00108368PHASE4COMPLETEDThe Effects of Risperidone and Olanzapine on Thinking
NCT00114595PHASE4COMPLETEDEthyl-Eicosapentaenoic Acid and Tardive Dyskinesia
NCT00130923PHASE4COMPLETEDRisperidone Long-acting Versus Oral Risperidone in Patients With Schizophrenia and Alcohol Use Disorder
NCT00137020PHASE4COMPLETEDClinical Effect Of Cross Titration Of Antipsychotics With Ziprasidone In Schizophrenia Or Schizoaffective Disorder
NCT00140166PHASE4COMPLETEDTreatment of Acute Schizophrenia With Vitamin Therapy
NCT00145847PHASE4COMPLETEDNaltrexone Treatment of Alcohol Abuse in Schizophrenia
NCT00148564PHASE4COMPLETEDEnergy Homeostasis Under Treatment With Atypical Antipsychotics
NCT00156715PHASE4COMPLETEDEfficacy of Quetiapine in the Treatment of Patients With Schizophrenia and a Comorbid Substance Use Disorder
NCT00158223PHASE4COMPLETEDEffectiveness of Pimozide in Augmenting the Effects of Clozapine in the Treatment of Schizophrenia
NCT00159081PHASE4COMPLETEDOne Year Drug Treatment in First-Episode Schizophrenia
NCT00159120PHASE4COMPLETEDMaintenance Treatment vs. Stepwise Drug Discontinuation in First-Episode Schizophrenia
NCT00159133PHASE4COMPLETEDProdrome-Based Early Intervention With Antipsychotics vs. Benzodiazepines in First-Episode Schizophrenia
NCT00159757PHASE4TERMINATED12 Week Open, Non-Comparative Switch Study Of Oral Ziprazidone In Previously Treated Schizophrenic Patients
NCT00167817PHASE4COMPLETEDEffect of Switch to Aripiprazole on Health and Smoking Parameters in Patients With Schizophrenia: A Pilot Study
NCT00169026PHASE4TERMINATEDAlcoholism and Schizophrenia: Effects of Clozapine
NCT00169039PHASE4TERMINATEDClozapine Versus Chlorpromazine for Treatment-Unresponsive Schizophrenia
NCT00169065PHASE4COMPLETEDEffectiveness of Clozapine Versus Olanzapine for Treatment-resistant Schizophrenia
NCT00169091PHASE4TERMINATEDClozapine Versus Haloperidol for Treating the First Episode of Schizophrenia
NCT00176423PHASE4COMPLETEDEfficacy Study of Galantamine for Cognitive Impairments in Schizophrenia
NCT00176436PHASE4COMPLETEDAtomoxetine for Treatment of Weight Gain in Olanzapine or Clozapine Patients
NCT00177008PHASE4COMPLETEDAripiprazole for the Treatment of Schizophrenia With Co-Morbid Social Anxiety