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SNX29

gene
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Also known as FLJ12363

Summary

SNX29 (sorting nexin 29, HGNC:30542) is a protein-coding gene on chromosome 16p13.13-p13.12, encoding Sorting nexin-29 (Q8TEQ0).

Predicted to enable phosphatidylinositol binding activity.

Source: NCBI Gene 92017 — RefSeq curated summary.

At a glance

  • GWAS associations: 24
  • Clinical variants (ClinVar): 138 total
  • Cancer driver (intOGen): activating (oncogene-like) across 2 cancer types
  • MANE Select transcript: NM_032167

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30542
Approved symbolSNX29
Namesorting nexin 29
Location16p13.13-p13.12
Locus typegene with protein product
StatusApproved
AliasesFLJ12363
Ensembl geneENSG00000048471
Ensembl biotypeprotein_coding
Entrez92017

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 9 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000562510, ENST00000563308, ENST00000564111, ENST00000564791, ENST00000566228, ENST00000568359, ENST00000568949, ENST00000569801, ENST00000892126, ENST00000892127, ENST00000892128, ENST00000892129, ENST00000892130

RefSeq mRNA: 2 — MANE Select: NM_032167 NM_001376490, NM_032167

CCDS: CCDS10553

Canonical transcript exons

ENST00000566228 — 21 exons

ExonStartEnd
ENSE000011617301252470212524841
ENSE000011617371240344812403529
ENSE000011617451239844612398501
ENSE000011617521235616312356279
ENSE000011617611227793312278036
ENSE000011617701219960112199683
ENSE000012030701247771912477859
ENSE000013217281207883312078915
ENSE000015568651206905712069132
ENSE000016319651212963012129758
ENSE000017462281212663312126696
ENSE000025897031197673411976813
ENSE000026131191256850612574287
ENSE000026220561205184712052222
ENSE000034974901204289712043077
ENSE000035120371204638412046454
ENSE000035280411202732012027444
ENSE000035829201200299112003043
ENSE000036275251199929711999358
ENSE000036537711204837212048620
ENSE000036899681206152812061646

Expression profiles

Bgee: expression breadth ubiquitous, 234 present calls, max score 93.87.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.3061 / max 199.7218, expressed in 1803 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
15281015.30611803

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
kidney epitheliumUBERON:000481993.87gold quality
sural nerveUBERON:001548893.11gold quality
upper arm skinUBERON:000426389.80silver quality
bone marrow cellCL:000209289.56gold quality
renal medullaUBERON:000036288.72gold quality
corpus callosumUBERON:000233688.01gold quality
lateral globus pallidusUBERON:000247687.48gold quality
layer of synovial tissueUBERON:000761687.38gold quality
adult mammalian kidneyUBERON:000008287.33gold quality
synovial jointUBERON:000221787.21gold quality
kidneyUBERON:000211386.99gold quality
tonsilUBERON:000237286.90gold quality
calcaneal tendonUBERON:000370186.50gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047386.24gold quality
subthalamic nucleusUBERON:000190685.46silver quality
left ventricle myocardiumUBERON:000656685.43gold quality
substantia nigra pars reticulataUBERON:000196685.28gold quality
cardiac muscle of right atriumUBERON:000337985.13gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099185.05gold quality
inferior vagus X ganglionUBERON:000536384.73silver quality
oral cavityUBERON:000016784.37gold quality
substantia nigra pars compactaUBERON:000196583.85gold quality
superficial temporal arteryUBERON:000161483.76silver quality
thymusUBERON:000237083.63silver quality
bronchial epithelial cellCL:000232883.35gold quality
cortical plateUBERON:000534383.10gold quality
bronchusUBERON:000218583.07gold quality
dorsal plus ventral thalamusUBERON:000189782.99silver quality
cortex of kidneyUBERON:000122582.96gold quality
leukocyteCL:000073882.83gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes9.78
E-GEOD-137537yes3.83

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

  • The strongest associated SNP in the combined analysis, including Danish and German-Dutch samples, was rs12922317 in RUNDC2A. (PMID:23358160)
  • SNX29, a new susceptibility gene shared with major mental disorders in Han Chinese population. (PMID:33143498)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriosnx29ENSDARG00000077317
mus_musculusSnx29ENSMUSG00000071669
rattus_norvegicusSnx29ENSRNOG00000002294
drosophila_melanogasterCG6051FBGN0039492
drosophila_melanogasterCG31064FBGN0051064
caenorhabditis_elegansWBGENE00003084

Paralogs (13): RUFY3 (ENSG00000018189), ZFYVE16 (ENSG00000039319), ZFYVE26 (ENSG00000072121), RUNDC3B (ENSG00000105784), RUNDC3A (ENSG00000108309), PLEKHM2 (ENSG00000116786), ZFYVE28 (ENSG00000159733), ZFYVE1 (ENSG00000165861), ZFYVE19 (ENSG00000166140), PLEKHF1 (ENSG00000166289), PLEKHF2 (ENSG00000175895), RUFY1 (ENSG00000176783), RUFY2 (ENSG00000204130)

Protein

Protein identifiers

Sorting nexin-29 — Q8TEQ0 (reviewed: Q8TEQ0)

Alternative names: RUN domain-containing protein 2A

All UniProt accessions (5): A0A0C4DGM3, Q8TEQ0, H3BPI1, H3BQF0, H3BT98

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the sorting nexin family.

Isoforms (2)

UniProt IDNamesCanonical?
Q8TEQ0-11yes
Q8TEQ0-22

RefSeq proteins (2): NP_001363419, NP_115543* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001683PX_domDomain
IPR004012Run_domDomain
IPR036871PX_dom_sfHomologous_superfamily
IPR037213Run_dom_sfHomologous_superfamily
IPR037916SNX29_PXDomain
IPR047329RUN_SNX29Domain

Pfam: PF00787, PF02759

UniProt features (22 total): modified residue 11, region of interest 3, domain 2, sequence conflict 2, chain 1, splice variant 1, coiled-coil region 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8TEQ0-F165.360.32

Functional residue map

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

Post-translational modifications (11): 292, 330, 344, 445, 450, 639, 641, 642, 646, 268, 291

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 144 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_DN, BROWNE_HCMV_INFECTION_48HR_DN, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, MILI_PSEUDOPODIA_CHEMOTAXIS_DN, GRYDER_PAX3FOXO1_TOP_ENHANCERS, GOMF_PHOSPHATIDYLINOSITOL_BINDING, GOMF_LIPID_BINDING, GOMF_PHOSPHOLIPID_BINDING, DODD_NASOPHARYNGEAL_CARCINOMA_DN, HORIUCHI_WTAP_TARGETS_UP, FORTSCHEGGER_PHF8_TARGETS_DN, PGF_UP.V1_DN, GSE14699_NAIVE_VS_DELETIONAL_TOLERANCE_CD8_TCELL_UP, GSE14415_FOXP3_KO_NATURAL_TREG_VS_TCONV_UP, GSE14415_INDUCED_TREG_VS_TCONV_DN

GO Biological Process (0):

GO Molecular Function (1): phosphatidylinositol binding (GO:0035091)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
anion binding1

Protein interactions and networks

STRING

780 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SNX29SNX21Q969T3600
SNX29SNX15Q9NRS6506
SNX29FAM43AQ8N2R8479
SNX29MSANTD1Q6ZTZ1478
SNX29ZMAT5Q9UDW3455
SNX29ANTXR2P58335452
SNX29TXNDC11Q6PKC3440
SNX29SNX20Q7Z614430
SNX29CAMTA2O94983430
SNX29SNX8Q9Y5X2424
SNX29GLMPQ8WWB7417
SNX29COG5Q9UP83415
SNX29FAM110AQ9BQ89414
SNX29PLEKHF2Q9H8W4410
SNX29SNX11Q9Y5W9401

IntAct

17 interactions, top by confidence:

ABTypeScore
KXD1HIP1psi-mi:“MI:0914”(association)0.530
DISC1AP4M1psi-mi:“MI:0914”(association)0.530
TRAF1ECI2psi-mi:“MI:0914”(association)0.350
CDC37ARHGAP10psi-mi:“MI:0914”(association)0.350
TFPTKRBA1psi-mi:“MI:0914”(association)0.350
SNX29GAPDHSpsi-mi:“MI:0914”(association)0.350
INSRBLTP3Bpsi-mi:“MI:0914”(association)0.350
RAB9ASNAP23psi-mi:“MI:2364”(proximity)0.270
TGOLN2BLTP3Bpsi-mi:“MI:2364”(proximity)0.270
SNX29psi-mi:“MI:0915”(physical association)0.000
SNX29psi-mi:“MI:0915”(physical association)0.000

BioGRID (57): SNX29 (Affinity Capture-MS), SNX29 (Affinity Capture-MS), SNX29 (Affinity Capture-MS), SNX29 (Affinity Capture-MS), SNX29 (Affinity Capture-MS), SNX29 (Affinity Capture-MS), SNX29 (Affinity Capture-MS), SNX29 (Affinity Capture-MS), SNX29 (Affinity Capture-RNA), SNX29 (Proximity Label-MS), SNX29 (Proximity Label-MS), SNX29 (Affinity Capture-RNA), SNX29 (Affinity Capture-MS), SNX29 (Proximity Label-MS), SNX29 (Proximity Label-MS)

ESM2 similar proteins: A0JMA8, A1L2S8, A4IG66, A7S7Z9, A8X2R2, A9ULX8, B3P7K6, E7F187, F1NVK6, F6UF99, G5EF60, O95071, O95159, P38349, P51592, P51950, P62447, P70302, P91682, P97496, Q0VFM0, Q16N38, Q1L0X2, Q1L8G6, Q20448, Q298N4, Q29EP6, Q2YDD3, Q4W9V0, Q56P03, Q5AX35, Q5BU09, Q5RFL4, Q5U245, Q62671, Q66IE4, Q6IQA2, Q6ZPS6, Q7YU29, Q80TP3

Diamond homologs: P40959, P57768, P57769, Q08DX0, Q3MPQ4, Q4FZZ1, Q559T8, Q5AG56, Q5PNP1, Q5R6Q7, Q5R7A7, Q5R903, Q7Z7A4, Q8BHY8, Q8BX57, Q8C080, Q8R4V0, Q8TEQ0, Q96BR1, Q9D3S3, Q9ERE3, Q9FG38, Q9Y5W7, Q9Y5W8, Q05B62, Q13596, Q4R503, Q6BIS2, Q99N27, Q9WV80, B1AVY7, Q08E29, Q0V9V7, Q4R7B9, Q5FVJ0, Q5NVC2, Q5PQS0, Q5R4V2, Q5R5R4, Q5U3W3

SIGNOR signaling

0 interactions.

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: activating (oncogene-like) across 2 cancer types — BLCA, SIC.

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance81
Likely benign10
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

6179 predictions. Top by Δscore:

VariantEffectΔscore
16:11976811:GCG:Gdonor_gain1.0000
16:11999357:AGGT:Adonor_loss1.0000
16:11999359:GT:Gdonor_loss1.0000
16:11999360:T:Gdonor_loss1.0000
16:12002989:A:AGacceptor_gain1.0000
16:12002990:G:GGacceptor_gain1.0000
16:12027318:AG:Aacceptor_gain1.0000
16:12027319:GG:Gacceptor_gain1.0000
16:12027441:ACAGG:Adonor_loss1.0000
16:12027442:CAGGT:Cdonor_loss1.0000
16:12027443:AG:Adonor_loss1.0000
16:12027444:GGTAC:Gdonor_loss1.0000
16:12027445:G:GCdonor_loss1.0000
16:12027446:T:Gdonor_loss1.0000
16:12043076:AGGTA:Adonor_loss1.0000
16:12043078:G:GGdonor_gain1.0000
16:12046375:A:AGacceptor_gain1.0000
16:12046375:AATCT:Aacceptor_gain1.0000
16:12046376:A:Gacceptor_gain1.0000
16:12046380:GCA:Gacceptor_loss1.0000
16:12046382:A:AGacceptor_gain1.0000
16:12046382:AG:Aacceptor_loss1.0000
16:12046383:G:GAacceptor_gain1.0000
16:12046383:GC:Gacceptor_gain1.0000
16:12046383:GCA:Gacceptor_gain1.0000
16:12046383:GCAC:Gacceptor_gain1.0000
16:12046383:GCACT:Gacceptor_gain1.0000
16:12046450:AGCAG:Adonor_loss1.0000
16:12046451:GCAG:Gdonor_gain1.0000
16:12046452:CAGGT:Cdonor_loss1.0000

AlphaMissense

5369 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:11999339:T:CL17P1.000
16:12002991:T:CC24R1.000
16:12003003:T:CF28L1.000
16:12003005:T:AF28L1.000
16:12003005:T:GF28L1.000
16:12003025:C:AA35D1.000
16:12027322:T:AV42D1.000
16:12043001:T:AW118R1.000
16:12043001:T:CW118R1.000
16:12048375:T:CL168P1.000
16:12048384:T:AI171K1.000
16:12048384:T:GI171R1.000
16:12048389:T:CF173L1.000
16:12048390:T:CF173S1.000
16:12048391:T:AF173L1.000
16:12048391:T:GF173L1.000
16:12199615:T:CL537P1.000
16:12199627:T:CL541P1.000
16:12199635:T:CY544H1.000
16:12199648:T:AV548D1.000
16:12278029:T:AL592H1.000
16:12278029:T:CL592P1.000
16:12356166:G:CA596P1.000
16:12356185:T:CL602P1.000
16:12356260:T:CL627P1.000
16:12524736:T:CL738P1.000
16:11999342:T:CL18P0.999
16:11999347:G:CA20P0.999
16:11999355:A:CK22N0.999
16:11999355:A:TK22N0.999

dbSNP variants (sampled 300 via entrez): RS1000000671 (16:12267520 C>T), RS1000001248 (16:12210713 T>A), RS1000004256 (16:12324670 A>G), RS1000004766 (16:12443334 G>A), RS1000007758 (16:12180744 C>T), RS1000007982 (16:12538662 C>G,T), RS1000008671 (16:12549601 C>G,T), RS1000010740 (16:12255636 C>G), RS1000016013 (16:12330868 C>G,T), RS1000017119 (16:12556464 G>A,T), RS1000024455 (16:12497897 G>A), RS1000028683 (16:12469967 C>T), RS1000029747 (16:12443281 C>A,T), RS1000037968 (16:12236784 A>G), RS1000039088 (16:12388971 A>G)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

24 associations (top):

StudyTraitp-value
GCST001762_71Obesity-related traits4.000000e-06
GCST001839_3Schizophrenia9.000000e-07
GCST002248_2Fasting insulin (dietary factor interaction)4.000000e-06
GCST002253_14Homeostasis model assessment of insulin resistance (dietary factor interaction)4.000000e-06
GCST002806_14Type 2 diabetes8.000000e-06
GCST003518_21Daytime sleep phenotypes2.000000e-06
GCST005316_507Intelligence (MTAG)2.000000e-08
GCST005586_1Breast milk fatty acid composition (maternal genotype effect)5.000000e-11
GCST005587_1Breast milk fatty acid composition (infant genotype effect)5.000000e-06
GCST005833_6Remission after SSRI treatment in MDD or openness3.000000e-07
GCST005834_6Response to SSRI in MDD or openness2.000000e-07
GCST006269_745General cognitive ability1.000000e-08
GCST006896_7Free thyroxine concentration8.000000e-09
GCST006979_249Heel bone mineral density9.000000e-10
GCST008595_100Cognitive ability, years of educational attainment or schizophrenia (pleiotropy)3.000000e-09
GCST008755_9Phenylephrine infusion rate during anesthesia5.000000e-06
GCST009322_6Numerical cognitive ability8.000000e-06
GCST009365_5LDL cholesterol levels x short total sleep time interaction (2df test)3.000000e-08
GCST011066_2Motor fluctuations in levodopa treated Parkinson’s disease8.000000e-06
GCST012490_133Femur bone mineral density x serum urate levels interaction2.000000e-08
GCST012490_615Femur bone mineral density x serum urate levels interaction9.000000e-09
GCST012498_10Autism4.000000e-06
GCST90000047_262Age at first sexual intercourse2.000000e-08
GCST90002394_536Monocyte percentage of white cells5.000000e-10

EFO canonical traits (17, from GWAS)

EFO IDTrait name
EFO:0008111diet measurement
EFO:0004501HOMA-IR
EFO:0007828daytime rest measurement
EFO:0004337intelligence
EFO:0005939parental genotype effect measurement
EFO:0007959fetal genotype effect measurement
EFO:0005658response to selective serotonin reuptake inhibitor
EFO:0007914openness measurement
EFO:0009270heel bone mineral density
EFO:0004784self reported educational attainment
EFO:0008354cognitive function measurement
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0010747response to levodopa
EFO:0010749motor function measurement
EFO:0004531urate measurement
EFO:0009749age at first sexual intercourse measurement
EFO:0007989monocyte percentage of leukocytes

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression, decreases methylation, increases methylation7
Aflatoxin B1affects expression, affects methylation, decreases expression, increases methylation5
bisphenol Aaffects cotreatment, increases methylation, decreases methylation, increases expression2
sodium arseniteincreases expression2
Cisplatindecreases expression, affects cotreatment2
aristolochic acid Idecreases expression1
afuresertibincreases expression1
FR900359increases phosphorylation1
methyleugenoldecreases expression1
triphenyl phosphateaffects expression1
trichostatin Aaffects expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
butyraldehydedecreases expression1
benzo(e)pyreneincreases methylation1
potassium chromate(VI)decreases expression, affects cotreatment1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, decreases expression1
aflatoxin B2affects methylation1
coumarinincreases phosphorylation1
epigallocatechin gallateaffects cotreatment, decreases expression1
bisphenol Saffects cotreatment, increases methylation1
jinfukangaffects cotreatment, decreases expression1
Resveratrolaffects cotreatment, increases expression1
Fulvestrantaffects cotreatment, increases methylation1
Acetaminophenincreases expression1
Carcinogensdecreases expression1
Coumestrolaffects cotreatment, decreases expression1
Melphalandecreases expression1
Methapyrileneincreases methylation1
Methyl Methanesulfonateincreases expression1
Mutagensdecreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.

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
v1.1.4
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