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SNX7

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Summary

SNX7 (sorting nexin 7, HGNC:14971) is a protein-coding gene on chromosome 1p21.3, encoding Sorting nexin-7 (Q9UNH6). Involved in the regulation of endocytosis and in several stages of intracellular trafficking.

This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. This protein does not contain a coiled coil region like some family members, and its exact function is unknown. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 11.

Source: NCBI Gene 51375 — RefSeq curated summary.

At a glance

  • GWAS associations: 15
  • Clinical variants (ClinVar): 76 total
  • MANE Select transcript: NM_015976

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14971
Approved symbolSNX7
Namesorting nexin 7
Location1p21.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000162627
Ensembl biotypeprotein_coding
OMIM614904
Entrez51375

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 10 protein_coding, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000306121, ENST00000454199, ENST00000473868, ENST00000528824, ENST00000529992, ENST00000851355, ENST00000851356, ENST00000851357, ENST00000924674, ENST00000971616, ENST00000971617, ENST00000971618

RefSeq mRNA: 3 — MANE Select: NM_015976 NM_001364903, NM_015976, NM_152238

CCDS: CCDS755, CCDS756

Canonical transcript exons

ENST00000306121 — 9 exons

ExonStartEnd
ENSE000012449949873823798738389
ENSE000018180149866172198661911
ENSE000034605469869551898695716
ENSE000034696779869870698698905
ENSE000034721069869107598691185
ENSE000034892949869153598691699
ENSE000034907539868488598685067
ENSE000035212079870181798701903
ENSE000036764289876005498760500

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 96.49.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 21.7693 / max 398.8763, expressed in 1509 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
41589.85401454
41606.27981348
41575.20571394
41590.4298244

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
tibiaUBERON:000097996.49gold quality
synovial jointUBERON:000221796.24gold quality
cartilage tissueUBERON:000241896.16gold quality
bronchial epithelial cellCL:000232895.72gold quality
jejunal mucosaUBERON:000039995.03gold quality
colonic mucosaUBERON:000031795.01gold quality
epithelium of bronchusUBERON:000203194.99gold quality
mucosa of sigmoid colonUBERON:000499394.78gold quality
bronchusUBERON:000218594.71gold quality
cortical plateUBERON:000534394.44gold quality
nephron tubuleUBERON:000123194.43gold quality
saphenous veinUBERON:000731894.34gold quality
calcaneal tendonUBERON:000370194.19gold quality
urethraUBERON:000005794.18gold quality
periodontal ligamentUBERON:000826693.57gold quality
germinal epithelium of ovaryUBERON:000130493.27gold quality
tendonUBERON:000004393.24gold quality
blood vessel layerUBERON:000479792.92gold quality
rectumUBERON:000105292.89gold quality
cauda epididymisUBERON:000436092.89gold quality
skin of hipUBERON:000155492.62gold quality
duodenumUBERON:000211492.61gold quality
esophagus squamous epitheliumUBERON:000692092.39gold quality
nasal cavity epitheliumUBERON:000538492.37gold quality
mammalian vulvaUBERON:000099792.18gold quality
palpebral conjunctivaUBERON:000181292.17gold quality
kidney epitheliumUBERON:000481992.09gold quality
popliteal arteryUBERON:000225092.05gold quality
tibial arteryUBERON:000761092.05gold quality
caput epididymisUBERON:000435891.83gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-MTAB-9388no8.60
E-ANND-3no0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

  • Overexpression of SNX7 in HEK293T cells reduces the levels of secreted Abeta and beta-cleaved N-terminal APP fragments (sAPPbeta). Moreover, SNX7 overexpression caused a significant reduction of the steady-state levels of APP as well as of the cell surface APP levels. (PMID:29080748)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriosnx7ENSDARG00000105185
mus_musculusSnx7ENSMUSG00000028007
rattus_norvegicusSnx7ENSRNOG00000017077

Paralogs (15): SNX11 (ENSG00000002919), SNX1 (ENSG00000028528), SNX10 (ENSG00000086300), SNX5 (ENSG00000089006), SNX8 (ENSG00000106266), SNX3 (ENSG00000112335), SNX4 (ENSG00000114520), SNX6 (ENSG00000129515), SNX9 (ENSG00000130340), SNX12 (ENSG00000147164), SNX30 (ENSG00000148158), SNX32 (ENSG00000172803), SNX33 (ENSG00000173548), SNX18 (ENSG00000178996), SNX2 (ENSG00000205302)

Protein

Protein identifiers

Sorting nexin-7 — Q9UNH6 (reviewed: Q9UNH6)

All UniProt accessions (4): B7ZC83, Q9UNH6, E9PLE1, E9PNL2

UniProt curated annotations — full annotation on UniProt →

Function. Involved in the regulation of endocytosis and in several stages of intracellular trafficking. Together with SNX4, involved in autophagosome assembly by regulating trafficking and recycling of phospholipid scramblase ATG9A.

Subunit / interactions. Heterodimer; heterodimerizes with SNX4.

Subcellular location. Early endosome membrane.

Similarity. Belongs to the sorting nexin family.

Isoforms (3)

UniProt IDNamesCanonical?
Q9UNH6-11yes
Q9UNH6-22
Q9UNH6-33

RefSeq proteins (3): NP_001351832, NP_057060, NP_689424 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001683PX_domDomain
IPR027267AH/BAR_dom_sfHomologous_superfamily
IPR036871PX_dom_sfHomologous_superfamily
IPR042130PX_SNX7Domain
IPR042131BAR_SNX7Domain

Pfam: PF00787

UniProt features (28 total): sequence conflict 8, helix 5, strand 4, binding site 4, domain 2, sequence variant 2, splice variant 2, chain 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
3IQ2X-RAY DIFFRACTION1.7

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UNH6-F186.330.69

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): 73; 75; 103; 117

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 138 (showing top): GOBP_REGULATION_OF_AUTOPHAGY, GOBP_VACUOLE_ORGANIZATION, GOBP_POSITIVE_REGULATION_OF_VACUOLE_ORGANIZATION, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN, HUMMERICH_MALIGNANT_SKIN_TUMOR_DN, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_REGULATION_OF_VACUOLE_ORGANIZATION, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_MACROAUTOPHAGY, GOBP_POSITIVE_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CATABOLIC_PROCESS, DOANE_RESPONSE_TO_ANDROGEN_DN

GO Biological Process (6): mitophagy (GO:0000423), protein transport (GO:0015031), endocytic recycling (GO:0032456), piecemeal microautophagy of the nucleus (GO:0034727), reticulophagy (GO:0061709), positive regulation of autophagosome assembly (GO:2000786)

GO Molecular Function (3): phosphatidylinositol binding (GO:0035091), protein binding (GO:0005515), lipid binding (GO:0008289)

GO Cellular Component (7): phagophore assembly site (GO:0000407), early endosome (GO:0005769), early endosome membrane (GO:0031901), cytoplasm (GO:0005737), endosome (GO:0005768), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
macroautophagy2
binding2
cytoplasm2
autophagy of mitochondrion1
transport1
intracellular protein localization1
establishment of protein localization1
endosomal transport1
vesicle-mediated transport to the plasma membrane1
microautophagy1
nucleophagy1
nucleus disassembly1
autophagosome assembly1
positive regulation of macroautophagy1
positive regulation of vacuole organization1
positive regulation of organelle assembly1
regulation of autophagosome assembly1
anion binding1
endosome1
early endosome1
endosome membrane1
intracellular anatomical structure1
endomembrane system1
cytoplasmic vesicle1
intracellular vesicle1

Protein interactions and networks

STRING

946 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SNX7SNX4O95219739
SNX7SNX32Q86XE0668
SNX7SNX6Q9UNH7567
SNX7SNX9Q9Y5X1551
SNX7PLPPR5Q32ZL2545
SNX7SNX17Q15036527
SNX7SNX27Q96L92488
SNX7SNX15Q9NRS6485
SNX7SNX8Q9Y5X2463
SNX7LRP8Q14114455
SNX7SNX22Q96L94450
SNX7KIF16BQ96L93431
SNX7VPS35Q96QK1414
SNX7AMPHP49418411
SNX7VPS29Q9UBQ0404

IntAct

35 interactions, top by confidence:

ABTypeScore
TEX11SNX7psi-mi:“MI:0915”(physical association)0.670
SNX7SNX4psi-mi:“MI:0914”(association)0.670
SNX7TEX11psi-mi:“MI:0915”(physical association)0.670
SNX7SNX4psi-mi:“MI:0915”(physical association)0.670
PDGFRBPIK3R2psi-mi:“MI:0914”(association)0.610
HGSSNX7psi-mi:“MI:0915”(physical association)0.560
SNX7HGSpsi-mi:“MI:0915”(physical association)0.560
LPAR1TMEM223psi-mi:“MI:0914”(association)0.530
SNX7BIRC3psi-mi:“MI:0915”(physical association)0.440
BIRC3SNX7psi-mi:“MI:0403”(colocalization)0.440
CRKSNX7psi-mi:“MI:0915”(physical association)0.400
GRB2SNX7psi-mi:“MI:0915”(physical association)0.400
NCK1SNX7psi-mi:“MI:0915”(physical association)0.400
SNX7PLCG1psi-mi:“MI:0915”(physical association)0.400
SNX7SNX6psi-mi:“MI:0915”(physical association)0.400
SNX7POLR2Lpsi-mi:“MI:0915”(physical association)0.370
HMOX2SNX7psi-mi:“MI:0915”(physical association)0.370
MESTSNX7psi-mi:“MI:0915”(physical association)0.370
MAGEA11SNX7psi-mi:“MI:0915”(physical association)0.370
NTRK3ILVBLpsi-mi:“MI:0914”(association)0.350
HLA-Cpsi-mi:“MI:0914”(association)0.350
SNX4SNX2psi-mi:“MI:0914”(association)0.350
CD226TMED7-TICAM2psi-mi:“MI:0914”(association)0.350
COMTD1TRIOpsi-mi:“MI:0914”(association)0.350

BioGRID (36): SNX7 (Two-hybrid), TEX11 (Two-hybrid), ASPM (Affinity Capture-MS), SNX4 (Affinity Capture-MS), DTNBP1 (Affinity Capture-MS), BLOC1S2 (Affinity Capture-MS), SNX7 (Two-hybrid), TEX11 (Two-hybrid), SNX4 (Affinity Capture-MS), DTNBP1 (Affinity Capture-MS), BLOC1S2 (Affinity Capture-MS), SNX7 (Two-hybrid), SNX7 (Two-hybrid), TBC1D21 (Two-hybrid), SNX7 (Proximity Label-MS)

ESM2 similar proteins: A0A324, B0KWE9, B1A924, B1MTH4, F6RQL9, O14817, O42602, O42603, O62772, O75954, P10063, P19019, P26048, P27681, P28472, P28473, P34998, P35347, P35353, P47866, P47869, P63138, Q09028, Q0VC00, Q13126, Q13324, Q3MHL3, Q49L09, Q4L208, Q4R5U9, Q5RAP3, Q5RCC5, Q5RF92, Q5ZJ75, Q60748, Q60972, Q76LL8, Q8JFQ2, Q8R4D1, Q8WU67

Diamond homologs: A0A098DRQ4, A6ZXL6, P0CR64, P0CR65, Q04053, Q07528, Q4R5U9, Q5AD73, Q5AZC9, Q6C9X0, Q6CNX6, Q6CWX3, Q759T1, Q75B65, Q7SB54, Q9CY18, Q9UNH6, A8WG21, F1Q506, O60493, O70492, O70493, P0CR60, P0CR61, Q08826, Q08DD7, Q0IIL5, Q1RMH8, Q2U4K2, Q4I1H6, Q4P1V3, Q4WWS3, Q522W5, Q566W7, Q5A748, Q5R5V1, Q5U211, Q6C2S9, Q6CY25, Q758Y7

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 29 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:

PathwayPartnersFoldFDR
Downstream signal transduction6114.2×2e-09

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance59
Likely benign1
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1520 predictions. Top by Δscore:

VariantEffectΔscore
1:98661907:GCAAG:Gdonor_gain1.0000
1:98661909:AAGGT:Adonor_loss1.0000
1:98661912:G:Tdonor_loss1.0000
1:98661913:T:Adonor_loss1.0000
1:98684879:TCTTA:Tacceptor_loss1.0000
1:98684883:A:AGacceptor_gain1.0000
1:98684883:A:Tacceptor_loss1.0000
1:98684883:AG:Aacceptor_gain1.0000
1:98684883:AGGAT:Aacceptor_gain1.0000
1:98684884:G:Aacceptor_gain1.0000
1:98684884:G:GAacceptor_gain1.0000
1:98684884:GGA:Gacceptor_gain1.0000
1:98684884:GGAT:Gacceptor_gain1.0000
1:98684884:GGATG:Gacceptor_gain1.0000
1:98685015:A:Tdonor_gain1.0000
1:98691064:A:AGacceptor_gain1.0000
1:98691065:C:Gacceptor_gain1.0000
1:98691073:A:AGacceptor_gain1.0000
1:98691073:AGA:Aacceptor_loss1.0000
1:98691074:G:GCacceptor_gain1.0000
1:98691074:GA:Gacceptor_gain1.0000
1:98691074:GAC:Gacceptor_gain1.0000
1:98691074:GACA:Gacceptor_gain1.0000
1:98691074:GACAT:Gacceptor_gain1.0000
1:98691181:TTCCA:Tdonor_gain1.0000
1:98691182:TCCA:Tdonor_gain1.0000
1:98691183:CCA:Cdonor_gain1.0000
1:98691183:CCAG:Cdonor_loss1.0000
1:98691184:CA:Cdonor_gain1.0000
1:98691184:CAG:Cdonor_loss1.0000

AlphaMissense

3018 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000120062 (1:98690859 C>A), RS1000256156 (1:98746432 G>A,T), RS1000258249 (1:98750671 T>C), RS1000284300 (1:98683968 C>G,T), RS1000323265 (1:98694301 C>T), RS1000393344 (1:98667827 A>G), RS1000432484 (1:98731228 T>A,C), RS1000449053 (1:98688570 C>T), RS1000450763 (1:98710899 A>G), RS1000452707 (1:98701776 A>G), RS1000465188 (1:98730877 C>T), RS1000485025 (1:98745779 G>A), RS1000497319 (1:98659509 G>A), RS1000531325 (1:98733113 T>C), RS1000559548 (1:98758454 A>G,T)

Disease associations

OMIM: gene MIM:614904 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

15 associations (top):

StudyTraitp-value
GCST001212_8Proinsulin levels2.000000e-07
GCST001786_10Dental caries2.000000e-06
GCST002938_1Copper levels1.000000e-07
GCST003469_3Response to cognitive-behavioural therapy in anxiety disorder9.000000e-06
GCST003542_176Night sleep phenotypes1.000000e-07
GCST003542_177Night sleep phenotypes8.000000e-07
GCST004029_15Angiotensin-converting enzyme inhibitor intolerance6.000000e-06
GCST004136_3Methadone dose in opioid dependence2.000000e-06
GCST004764_2LDL cholesterol change in response to fenofibrate in statin-treated type 2 diabetes8.000000e-07
GCST005359_6Disease progression in age-related macular degeneration8.000000e-06
GCST007325_201General risk tolerance (MTAG)2.000000e-08
GCST008359_4Response to cognitive-behavioural therapy in anxiety disorder2.000000e-06
GCST009863_1Insulin-related traits (multivariate analysis)2.000000e-10
GCST010796_3498Electrocardiogram morphology (amplitude at temporal datapoints)3.000000e-08
GCST011494_86Daytime nap6.000000e-08

EFO canonical traits (9, from GWAS)

EFO IDTrait name
EFO:0004467insulin measurement
EFO:0007820cognitive behavioural therapy
EFO:0005325response to angiotensin-converting enzyme inhibitor
EFO:0007907methadone dose measurement
EFO:0007804LDL cholesterol change measurement
EFO:0008336disease progression measurement
EFO:0008579risk-taking behaviour
EFO:0004327electrocardiography
EFO:0007828daytime rest measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression2
dicrotophosdecreases expression1
arseniteaffects binding, increases reaction1
perfluorooctane sulfonic aciddecreases expression1
CGP 52608affects binding, increases reaction1
abrinedecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Antimycin Adecreases expression1
Benzo(a)pyrenedecreases methylation1
Doxorubicindecreases expression1
Hydrogen Peroxideaffects expression1
Quercetindecreases expression1
Rotenonedecreases expression1
Asbestos, Serpentineincreases methylation1
Cadmium Chloridedecreases expression1
Copper Sulfatedecreases expression1
Lactic Aciddecreases expression1
Particulate Matterdecreases expression, increases abundance1

Clinical trials (associated diseases)

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

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.2
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot