SNX16

gene
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Summary

SNX16 (sorting nexin 16, HGNC:14980) is a protein-coding gene on chromosome 8q21.13, encoding Sorting nexin-16 (P57768). May be involved 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. The protein encoded by this gene associates with late endosome membranes as is involved in tubule formation, cholesterol transport, and transport of tetraspanin CD81. The encoded protein also inhibits cell migration and tumorigenesis.

Source: NCBI Gene 64089 — RefSeq curated summary.

At a glance

  • GWAS associations: 15
  • Clinical variants (ClinVar): 49 total
  • MANE Select transcript: NM_152836

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14980
Approved symbolSNX16
Namesorting nexin 16
Location8q21.13
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000104497
Ensembl biotypeprotein_coding
OMIM614903
Entrez64089

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 20 protein_coding, 1 retained_intron

ENST00000345957, ENST00000353788, ENST00000396330, ENST00000518183, ENST00000519119, ENST00000519212, ENST00000519817, ENST00000520618, ENST00000521773, ENST00000521810, ENST00000523757, ENST00000856552, ENST00000856553, ENST00000856554, ENST00000856555, ENST00000944857, ENST00000944858, ENST00000944859, ENST00000944860, ENST00000944861, ENST00000944862

RefSeq mRNA: 4 — MANE Select: NM_152836 NM_001348189, NM_022133, NM_152836, NM_152837

CCDS: CCDS6234, CCDS6235

Canonical transcript exons

ENST00000345957 — 8 exons

ExonStartEnd
ENSE000006981858180238081802499
ENSE000006981868180309281803228
ENSE000010167798182943081829516
ENSE000012065928181532581815394
ENSE000012118548183961281840082
ENSE000021245248179958381801593
ENSE000021315868184212281842185
ENSE000037903318182379281823940

Expression profiles

Bgee: expression breadth ubiquitous, 257 present calls, max score 97.34.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.1422 / max 88.0861, expressed in 1507 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
937802.36661037
937811.5787933
937840.6578376
937830.3065185
937820.2327127

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
spermCL:000001997.34gold quality
male germ cellCL:000001593.22gold quality
secondary oocyteCL:000065590.03gold quality
lower esophagus mucosaUBERON:003583486.82gold quality
skin of hipUBERON:000155486.71gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099186.30gold quality
esophagus squamous epitheliumUBERON:000692086.19gold quality
gingival epitheliumUBERON:000194985.21gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047385.07gold quality
monocyteCL:000057684.48gold quality
germinal epithelium of ovaryUBERON:000130484.23gold quality
Brodmann (1909) area 23UBERON:001355483.90gold quality
oocyteCL:000002383.89gold quality
gall bladderUBERON:000211083.71gold quality
parietal pleuraUBERON:000240083.67gold quality
mononuclear cellCL:000084283.61gold quality
gingivaUBERON:000182883.19gold quality
esophagus mucosaUBERON:000246983.05gold quality
visceral pleuraUBERON:000240182.88gold quality
leukocyteCL:000073882.85gold quality
pleuraUBERON:000097781.93gold quality
islet of LangerhansUBERON:000000681.32gold quality
amniotic fluidUBERON:000017381.17gold quality
epithelium of esophagusUBERON:000197680.83gold quality
cortical plateUBERON:000534380.61gold quality
upper leg skinUBERON:000426280.49gold quality
calcaneal tendonUBERON:000370180.28gold quality
esophagusUBERON:000104380.13gold quality
adipose tissueUBERON:000101379.88gold quality
smooth muscle tissueUBERON:000113579.87gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no3.79

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

182 targeting SNX16, 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-1277-5P100.0073.955056
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-5692A100.0074.406850
HSA-MIR-429100.0073.442698
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-3646100.0073.565283
HSA-MIR-196A-5P100.0068.16684
HSA-MIR-196B-5P100.0068.16681
HSA-MIR-8485100.0077.574731
HSA-MIR-340-5P100.0072.504437
HSA-MIR-9-5P100.0072.282361
HSA-MIR-3163100.0077.238605
HSA-MIR-656-3P100.0072.152788
HSA-MIR-3924100.0072.092394
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-450099.9972.722367
HSA-MIR-366299.9973.825684
HSA-MIR-548N99.9871.944170
HSA-MIR-1213699.9872.815713
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-548P99.9872.253784

Literature-anchored findings (GeneRIF, showing 6)

  • SNX16 is a sorting nexin that may function in the trafficking of proteins between the early and late endosomal compartments (PMID:12813048)
  • SNX16 regulates the recycling trafficking of E-cadherin . SNX16 associates with the cytoplasmic domain of E-cadherin via PPII/alpha2 loop. (PMID:28712807)
  • SNX16 activates c-Myc signaling by inhibiting ubiquitin-mediated proteasomal degradation of eEF1A2 in colorectal cancer development. (PMID:31876369)
  • BHLHE40 plays a pathological role in pre-eclampsia through upregulating SNX16 by transcriptional inhibition of miR-196a-5p. (PMID:32579212)
  • [Sorting Nexin 16:Structure,Function,and Role in Diseases]. (PMID:36373636)
  • SNX16 is required for hepatocellular carcinoma survival via modulating the EGFR-AKT signaling pathway. (PMID:38849490)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriosnx16ENSDARG00000046072
mus_musculusSnx16ENSMUSG00000027534
rattus_norvegicusSnx16ENSRNOG00000009953
drosophila_melanogasterSnx16FBGN0034265

Paralogs (1): PXK (ENSG00000168297)

Protein

Protein identifiers

Sorting nexin-16P57768 (reviewed: P57768)

All UniProt accessions (8): P57768, E5RG30, E5RGQ6, E5RGS8, E5RH07, E5RHF1, E5RJ65, E5RJ81

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in several stages of intracellular trafficking. Plays a role in protein transport from early to late endosomes. Plays a role in protein transport to the lysosome. Promotes degradation of EGFR after EGF signaling. Plays a role in intracellular transport of vesicular stomatitis virus nucleocapsids from the endosome to the cytoplasm.

Subunit / interactions. Homooligomer. Interacts with EGFR.

Subcellular location. Early endosome membrane. Late endosome membrane. Cytoplasm. Lysosome.

Tissue specificity. Detected in placenta, lung, liver,heart and pancreas.

Domain organisation. The PX domain mediates interaction with membranes enriched in phosphatidylinositol 3-phosphate.

Similarity. Belongs to the sorting nexin family.

Isoforms (2)

UniProt IDNamesCanonical?
P57768-11yes
P57768-22

RefSeq proteins (4): NP_001335118, NP_071416, NP_690049, NP_690050 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001683PX_domDomain
IPR036871PX_dom_sfHomologous_superfamily
IPR037911SNX16_PXDomain
IPR051837SortingNexin/PXDomain-PKLikeFamily

Pfam: PF00787

UniProt features (29 total): helix 6, strand 5, compositionally biased region 4, binding site 3, mutagenesis site 2, region of interest 2, chain 1, domain 1, modified residue 1, splice variant 1, sequence variant 1, sequence conflict 1, coiled-coil region 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
5GW0X-RAY DIFFRACTION3.3
5GW1X-RAY DIFFRACTION3.35

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P57768-F171.420.42

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 (3): 146; 184; 144

Post-translational modifications (1): 222

Mutagenesis-validated functional residues (2):

PositionPhenotype
144abolishes binding to membranes enriched in phosphatidylinositol 3-phosphate.
145abolishes binding to phosphatidylinositol 3-phosphate.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 245 (showing top): ACTACCT_MIR196A_MIR196B, GOBP_LYSOSOMAL_TRANSPORT, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, TGCACTT_MIR519C_MIR519B_MIR519A, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOZGIT_ESR1_TARGETS_DN, GOBP_ENDOSOME_TO_LYSOSOME_TRANSPORT, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_PROTEIN_TARGETING, GOBP_VACUOLAR_TRANSPORT, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ORGANELLE, BONCI_TARGETS_OF_MIR15A_AND_MIR16_1

GO Biological Process (5): receptor recycling (GO:0001881), protein targeting to lysosome (GO:0006622), endosome to lysosome transport (GO:0008333), early endosome to late endosome transport (GO:0045022), protein transport (GO:0015031)

GO Molecular Function (3): phosphatidylinositol binding (GO:0035091), identical protein binding (GO:0042802), lipid binding (GO:0008289)

GO Cellular Component (9): lysosome (GO:0005764), early endosome (GO:0005769), late endosome (GO:0005770), endosome membrane (GO:0010008), early endosome membrane (GO:0031901), late endosome membrane (GO:0031902), cytoplasm (GO:0005737), endosome (GO:0005768), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
endosome3
lysosomal transport2
endosome membrane2
cellular anatomical structure2
endocytosis1
receptor metabolic process1
protein targeting to vacuole1
protein localization to lysosome1
intercellular transport1
vesicle-mediated transport1
cytoplasm1
vesicle-mediated transport between endosomal compartments1
transport1
intracellular protein localization1
establishment of protein localization1
anion binding1
protein binding1
binding1
lytic vacuole1
cytoplasmic vesicle membrane1
bounding membrane of organelle1
early endosome1
late endosome1
intracellular anatomical structure1
endomembrane system1
cytoplasmic vesicle1

Protein interactions and networks

STRING

646 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SNX16FCHSD2O94868749
SNX16VPS26AO75436676
SNX16FCHSD1Q86WN1576
SNX16SNX15Q9NRS6561
SNX16SNX1Q13596557
SNX16SNX17Q15036551
SNX16SNX20Q7Z614540
SNX16SNX3O60493530
SNX16SNX11Q9Y5W9519
SNX16SNX21Q969T3505
SNX16SNX27Q96L92505
SNX16SNX24Q9Y343478
SNX16SNX2P82862475
SNX16ALS2CLQ60I27474
SNX16SNX9Q9Y5X1473

IntAct

10 interactions, top by confidence:

ABTypeScore
YEATS4ZNHIT1psi-mi:“MI:0914”(association)0.790
ZNF175SNX16psi-mi:“MI:0915”(physical association)0.400
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
KIF6ACADSpsi-mi:“MI:0914”(association)0.350
SNX16POTEFpsi-mi:“MI:0914”(association)0.350
ZNF778LRP4psi-mi:“MI:0914”(association)0.350
ZNF767PZMYM6psi-mi:“MI:0914”(association)0.350

BioGRID (53): SNX16 (Affinity Capture-MS), SNX16 (Affinity Capture-MS), SNX16 (Affinity Capture-MS), SNX16 (Affinity Capture-MS), SNX16 (Affinity Capture-MS), SNX16 (Affinity Capture-MS), SNX16 (Affinity Capture-MS), SNX16 (Affinity Capture-MS), SNX16 (Synthetic Lethality), SNX16 (Affinity Capture-MS), TBC1D2B (Affinity Capture-MS), SNX16 (Affinity Capture-MS), YEATS4 (Affinity Capture-MS), SNX16 (Affinity Capture-MS), SNX16 (Affinity Capture-MS)

ESM2 similar proteins: A0A1L8GR68, A2CG63, A2VE56, D3ZHS6, E6ZGB4, F7AQ22, O75376, O88974, P0C6S7, P57768, P57769, Q15047, Q2YDJ8, Q2YDW7, Q4KKX4, Q4LE39, Q52L14, Q5F3F2, Q5F3N6, Q5FWF5, Q5R6Q7, Q5VVJ2, Q60974, Q66JB6, Q68FE8, Q69Z61, Q69Z66, Q69Z69, Q6N043, Q6NXK2, Q7Z6G8, Q86YI8, Q8BIZ1, Q8C080, Q8K2W6, Q8QFX1, Q92560, Q96N64, Q98925, Q99PU7

Diamond homologs: A0A1B7YDZ4, A1A4L0, A7TKX9, I1RXT2, O60493, O70492, O70493, O95219, P0CR60, P0CR61, P0CR62, P0CR63, P40959, P47057, P57768, P57769, Q08DD7, Q1RMH8, Q28E02, Q2U4K2, Q2UB56, Q3MPQ4, Q4I1H6, Q4P1V3, Q4R5U9, Q4V7P7, Q4WWS3, Q4WZF1, Q5A748, Q5AD77, Q5R4C2, Q5R5V1, Q5R6Q7, Q5U211, Q6BHN9, Q6BIS2, Q6C2S9, Q6CHY6, Q6CUC4, Q6FNH2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance37
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1835 predictions. Top by Δscore:

VariantEffectΔscore
8:81801589:CAGCT:Cacceptor_gain1.0000
8:81801590:AGCT:Aacceptor_gain1.0000
8:81801592:CT:Cacceptor_gain1.0000
8:81801593:TC:Tacceptor_loss1.0000
8:81801594:C:CAacceptor_loss1.0000
8:81801594:C:CCacceptor_gain1.0000
8:81802375:TATA:Tdonor_loss1.0000
8:81802376:ATACC:Adonor_loss1.0000
8:81802377:TA:Tdonor_loss1.0000
8:81802378:A:ACdonor_gain1.0000
8:81802378:A:Cdonor_loss1.0000
8:81802379:C:Adonor_loss1.0000
8:81802379:C:CCdonor_gain1.0000
8:81802382:AGATT:Adonor_gain1.0000
8:81802383:G:Cdonor_gain1.0000
8:81802495:ATGTT:Aacceptor_gain1.0000
8:81802496:TGTT:Tacceptor_gain1.0000
8:81802497:GTT:Gacceptor_gain1.0000
8:81802500:C:CCacceptor_gain1.0000
8:81803090:A:ACdonor_gain1.0000
8:81803090:A:Cdonor_loss1.0000
8:81803091:C:Adonor_loss1.0000
8:81803091:C:CCdonor_gain1.0000
8:81803133:A:ACdonor_gain1.0000
8:81803134:C:CCdonor_gain1.0000
8:81803224:AATGC:Aacceptor_gain1.0000
8:81803225:ATGC:Aacceptor_gain1.0000
8:81803226:TGC:Tacceptor_gain1.0000
8:81803227:GC:Gacceptor_gain1.0000
8:81803228:CC:Cacceptor_gain1.0000

AlphaMissense

2273 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
8:81815376:A:CF210L1.000
8:81815376:A:TF210L1.000
8:81815377:A:CF210C1.000
8:81815377:A:GF210S1.000
8:81815378:A:GF210L1.000
8:81823828:A:GL192P1.000
8:81823830:A:CF191L1.000
8:81823830:A:TF191L1.000
8:81823831:A:GF191S1.000
8:81823832:A:GF191L1.000
8:81823840:A:GL188S1.000
8:81823851:T:AR184S1.000
8:81823851:T:GR184S1.000
8:81823852:C:AR184I1.000
8:81823852:C:GR184T1.000
8:81823853:T:CR184G1.000
8:81823861:A:GL181S1.000
8:81823863:A:CF180L1.000
8:81823863:A:TF180L1.000
8:81823864:A:GF180S1.000
8:81823865:A:GF180L1.000
8:81823896:T:AK169N1.000
8:81823896:T:GK169N1.000
8:81823897:T:AK169I1.000
8:81823939:A:GL155S1.000
8:81829440:A:GL151P1.000
8:81829449:A:GF148S1.000
8:81829458:T:CY145C1.000
8:81829459:A:CY145D1.000
8:81829459:A:GY145H1.000

dbSNP variants (sampled 300 via entrez): RS1000002069 (8:81823677 T>C), RS1000028372 (8:81804775 A>T), RS1000162910 (8:81804058 T>C), RS1000256582 (8:81816598 G>A,T), RS1000332455 (8:81820727 C>G), RS1000426403 (8:81816935 T>A,C), RS1000689781 (8:81834986 C>T), RS1000701653 (8:81803731 A>C), RS1000841076 (8:81828370 T>C,G), RS1000874456 (8:81822268 G>A,C), RS1000948068 (8:81829265 T>C), RS1000974131 (8:81806640 C>T), RS1000992596 (8:81799326 A>C), RS1001006840 (8:81821977 C>T), RS1001111505 (8:81806351 T>C)

Disease associations

OMIM: gene MIM:614903 | 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
GCST000675_12Heart failure3.000000e-06
GCST001941_13Ovarian cancer6.000000e-09
GCST001941_17Ovarian cancer7.000000e-10
GCST002408_5Response to methotrexate in juvenile idiopathic arthritis3.000000e-06
GCST002408_6Response to methotrexate in juvenile idiopathic arthritis2.000000e-06
GCST004642_3QT interval (ambient particulate matter interaction)2.000000e-06
GCST006988_108Blond vs. brown/black hair color1.000000e-22
GCST006989_32Brown vs. black hair color1.000000e-13
GCST007094_167Diastolic blood pressure4.000000e-10
GCST007099_155Systolic blood pressure3.000000e-06
GCST007158_6Refractive astigmatism6.000000e-06
GCST008505_1Fasting glucose change (short-term)1.000000e-06
GCST009442_9Age-related cognitive decline (executive function) (slope of z-scores)2.000000e-06
GCST012115_2Rheumatic heart disease4.000000e-07
GCST012117_3Rheumatic heart disease1.000000e-06

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0004682QT interval
EFO:0008255particulate matter air pollution measurement
EFO:0003924hair color
EFO:0006336diastolic blood pressure
EFO:0006335systolic blood pressure
EFO:0007710cognitive decline measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, increases expression, increases methylation3
trichostatin Aaffects cotreatment, decreases expression2
sodium arseniteaffects cotreatment, increases abundance, increases expression2
perfluorooctane sulfonic aciddecreases expression2
Air Pollutantsincreases abundance, increases expression, decreases expression2
Valproic Aciddecreases methylation, increases expression2
Cyclosporineincreases expression2
Particulate Matterincreases abundance, increases expression, decreases expression2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
FR900359increases phosphorylation1
bisphenol Adecreases expression1
2,4,5,2’,4’,5’-hexachlorobiphenyldecreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
N-acetyl-4-benzoquinoneimineaffects response to substance1
di-n-butylphosphoric acidaffects expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
14-deoxy-11,12-didehydroandrographolideincreases expression1
abrineincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidineincreases expression, increases response to substance1
jinfukangdecreases expression1
NSC 689534affects binding, increases expression1
Leflunomideincreases expression1
Arsenicaffects cotreatment, increases abundance, increases expression1
Atrazinedecreases expression1
Copperaffects binding, increases expression1
Drugs, Chinese Herbalincreases expression1
Ethyl Methanesulfonateincreases expression1
Formaldehydeincreases expression1

Clinical trials (associated diseases)

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