TMEM39A

gene
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Also known as FLJ10902SUSR2

Summary

TMEM39A (transmembrane protein 39A, HGNC:25600) is a protein-coding gene on chromosome 3q13.33, encoding Transmembrane protein 39A (Q9NV64). Regulates autophagy by controlling the spatial distribution and levels of the intracellular phosphatidylinositol 4-phosphate (PtdIns(4)P) pools.

Involved in negative regulation of autophagosome assembly; negative regulation of autophagosome maturation; and positive regulation of viral genome replication. Located in endoplasmic reticulum membrane.

Source: NCBI Gene 55254 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 55 total
  • MANE Select transcript: NM_018266

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25600
Approved symbolTMEM39A
Nametransmembrane protein 39A
Location3q13.33
Locus typegene with protein product
StatusApproved
AliasesFLJ10902, SUSR2
Ensembl geneENSG00000176142
Ensembl biotypeprotein_coding
Entrez55254

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 17 protein_coding, 3 nonsense_mediated_decay, 2 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000319172, ENST00000438581, ENST00000461654, ENST00000468545, ENST00000468676, ENST00000473684, ENST00000482162, ENST00000486159, ENST00000486235, ENST00000490099, ENST00000491685, ENST00000497993, ENST00000884856, ENST00000884857, ENST00000884858, ENST00000884859, ENST00000884860, ENST00000924820, ENST00000924821, ENST00000924822, ENST00000924823, ENST00000955953, ENST00000955954, ENST00000955955

RefSeq mRNA: 1 — MANE Select: NM_018266 NM_018266

CCDS: CCDS2987

Canonical transcript exons

ENST00000319172 — 9 exons

ExonStartEnd
ENSE00001857038119463336119463615
ENSE00003472202119436791119436978
ENSE00003560311119437755119438103
ENSE00003577939119428949119432214
ENSE00003581208119434762119434882
ENSE00003630088119461962119462148
ENSE00003784324119447018119447172
ENSE00003785531119452447119452530
ENSE00003789003119458018119458240

Expression profiles

Bgee: expression breadth ubiquitous, 255 present calls, max score 96.33.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 34.5272 / max 450.1498, expressed in 1820 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
4398332.74961813
439850.6041276
439840.4368193
439880.313999
439860.255449
439870.090530
439820.076927

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
stromal cell of endometriumCL:000225596.33gold quality
body of pancreasUBERON:000115095.82gold quality
tibiaUBERON:000097993.51gold quality
pancreasUBERON:000126492.79gold quality
right lungUBERON:000216792.10gold quality
calcaneal tendonUBERON:000370192.07gold quality
upper lobe of left lungUBERON:000895291.79gold quality
right lobe of thyroid glandUBERON:000111991.66gold quality
left lobe of thyroid glandUBERON:000112091.62gold quality
colonic epitheliumUBERON:000039791.26gold quality
cartilage tissueUBERON:000241891.26gold quality
endocervixUBERON:000045891.00gold quality
upper lobe of lungUBERON:000894890.99gold quality
thyroid glandUBERON:000204690.78gold quality
gall bladderUBERON:000211090.57gold quality
tibial nerveUBERON:000132390.43gold quality
adenohypophysisUBERON:000219690.39gold quality
minor salivary glandUBERON:000183090.37gold quality
pituitary glandUBERON:000000790.31gold quality
body of uterusUBERON:000985390.19gold quality
right ovaryUBERON:000211890.15gold quality
omental fat padUBERON:001041489.78gold quality
peritoneumUBERON:000235889.76gold quality
adrenal tissueUBERON:001830389.66gold quality
monocyteCL:000057689.62gold quality
saliva-secreting glandUBERON:000104489.60gold quality
left ovaryUBERON:000211989.59gold quality
right atrium auricular regionUBERON:000663189.53gold quality
islet of LangerhansUBERON:000000689.42gold quality
mononuclear cellCL:000084289.40gold 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)

112 targeting TMEM39A, 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-1277-5P100.0073.955056
HSA-MIR-340-5P100.0072.504437
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-12118100.0065.881270
HSA-MIR-656-3P100.0072.152788
HSA-MIR-4682100.0068.891258
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-3173-3P99.9866.491217
HSA-MIR-6891-5P99.9866.531372
HSA-MIR-480399.9871.993117
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-60799.9773.625593
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-495-3P99.9672.814197
HSA-MIR-568899.9673.234504
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-570-3P99.9672.414910
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-1236-3P99.9468.041695
HSA-MIR-4778-3P99.9370.401818
HSA-MIR-381-3P99.9371.872854
HSA-MIR-1-3P99.9372.351914

Literature-anchored findings (GeneRIF, showing 6)

  • Comprehensive follow-up of the first genome-wide association study of multiple sclerosis identifies TMEM39A as susceptibility (PMID:20007504)
  • Pooled analysis corroborated the effect on multiple sclerosis predisposition of three genes: TMEM39A, IL12B, and CBLB (PMID:22194214)
  • Four additional susceptibility loci (IRF8, TMEM39A, IKZF3, and ZPBP2) for systemic lupus erythematosus were robustly established a multiethnic population (European, African American, Asian, Hispanic, Gullah, and Amerindian). (PMID:22464253)
  • Findings identified three novel associations in SNPs located in the TMEM39A gene associated with systemic lupus erythematous susceptibility in a Chinese Han population. (PMID:28427360)
  • TMEM39A mRNA expression may be associated with the development and/or course of multiple sclerosis. rs1132200 and rs17281647 were not associated with multiple sclerosis. (PMID:28444502)
  • Polymorphisms of the TMEM39A gene are associated with the susceptibility to Autoimmune Thyroid diseases (AITD), especially for early-onset AITD and Hashimoto thyroiditis with hypothyroidism. (PMID:31553233)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriotmem39aENSDARG00000102746
mus_musculusTmem39aENSMUSG00000002845
rattus_norvegicusTmem39aENSRNOG00000003075
drosophila_melanogasterCG13016FBGN0033899
caenorhabditis_eleganstmem-39WBGENE00017003

Paralogs (1): TMEM39B (ENSG00000121775)

Protein

Protein identifiers

Transmembrane protein 39AQ9NV64 (reviewed: Q9NV64)

All UniProt accessions (7): Q9NV64, C9IYN1, C9JUZ6, C9JYN8, C9K0C7, F8WAU1, H7C5P7

UniProt curated annotations — full annotation on UniProt →

Function. Regulates autophagy by controlling the spatial distribution and levels of the intracellular phosphatidylinositol 4-phosphate (PtdIns(4)P) pools. Modulates (PtdIns(4)P) levels by regulating the ER-to-Golgi trafficking of the phosphatidylinositide phosphatase SACM1L. (Microbial infection) Positively regulates the replication of encephalomyocarditis virus (EMCV) via autophagy-dependent pathway.

Subunit / interactions. Interacts with SACM1L, SEC23A and SEC24A. (Microbial infection) Interacts with encephalomyocarditis virus (EMCV) major capsid proteins VP1 and VP2.

Subcellular location. Endoplasmic reticulum membrane.

Tissue specificity. Up-regulated in brain tumor glioblastoma multiforme cells (at protein level).

Similarity. Belongs to the TMEM39 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9NV64-11yes
Q9NV64-22

RefSeq proteins (1): NP_060736* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR019397Uncharacterised_TMEM39Family

Pfam: PF10271

UniProt features (16 total): transmembrane region 8, glycosylation site 2, splice variant 2, sequence variant 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NV64-F174.800.30

Functional residue map

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

Glycosylation sites (2): 39, 31

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 242 (showing top): ATF_B, GOBP_REGULATION_OF_AUTOPHAGY, TGCGCANK_UNKNOWN, GOBP_VACUOLE_ORGANIZATION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_POSITIVE_REGULATION_OF_VIRAL_GENOME_REPLICATION, GOBP_REGULATION_OF_VACUOLE_ORGANIZATION, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_NEGATIVE_REGULATION_OF_ORGANELLE_ASSEMBLY, GOBP_MACROAUTOPHAGY, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, CREB_Q4, GOBP_NEGATIVE_REGULATION_OF_AUTOPHAGY, GOBP_REGULATION_OF_CATABOLIC_PROCESS

GO Biological Process (4): autophagy (GO:0006914), positive regulation of viral genome replication (GO:0045070), negative regulation of autophagosome maturation (GO:1901097), negative regulation of autophagosome assembly (GO:1902902)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (3): endoplasmic reticulum membrane (GO:0005789), endoplasmic reticulum (GO:0005783), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
negative regulation of macroautophagy2
catabolic process1
transmembrane transport1
process utilizing autophagic mechanism1
viral genome replication1
regulation of viral genome replication1
positive regulation of viral process1
negative regulation of protein-containing complex disassembly1
autophagosome maturation1
regulation of autophagosome maturation1
autophagosome assembly1
negative regulation of organelle assembly1
regulation of autophagosome assembly1
binding1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
cellular anatomical structure1

Protein interactions and networks

STRING

538 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
TMEM39ACLEC16AQ2KHT3527
TMEM39AARHGAP31Q2M1Z3520
TMEM39ASEC24BO95487518
TMEM39ATIMMDC1Q9NPL8507
TMEM39ACHRNA9Q9UGM1466
TMEM39AKIF21BO75037442
TMEM39AIQCJQ1A5X6419
TMEM39APOU2AF2Q8IXP5400
TMEM39AEVI5O60447399
TMEM39AZPBP2Q6X784399
TMEM39AMACIRQ96GV9398
TMEM39APOGLUT1Q8NBL1397
TMEM39AEXOC3L4Q17RC7391
TMEM39ATMEM25Q86YD3389
TMEM39ACFAP263Q9H0I3367
TMEM39AOR8D4Q8NGM9367

IntAct

64 interactions, top by confidence:

ABTypeScore
GABREFZD6psi-mi:“MI:0914”(association)0.530
ZNRF4UPK3BL1psi-mi:“MI:0914”(association)0.530
ZACNGPAA1psi-mi:“MI:0914”(association)0.530
TCTN2TPST2psi-mi:“MI:0914”(association)0.530
GAAB3GAT3psi-mi:“MI:0914”(association)0.530
TM2D2TMEM97psi-mi:“MI:0914”(association)0.530
IL9RRETSATpsi-mi:“MI:0914”(association)0.530
FBXO2TMEM131Lpsi-mi:“MI:0914”(association)0.530
LRRTM1UPK3BL1psi-mi:“MI:0914”(association)0.530
CHRNA9CHEK1psi-mi:“MI:0914”(association)0.530
B4GAT1ADCY6psi-mi:“MI:0914”(association)0.530
CHRNDTPST2psi-mi:“MI:0914”(association)0.530
ADAM21PLXNA2psi-mi:“MI:0914”(association)0.530
FKBP2TTC13psi-mi:“MI:0914”(association)0.530
TMEM39Areppsi-mi:“MI:0915”(physical association)0.370
UPK1ATMEM223psi-mi:“MI:0914”(association)0.350
LRRTM1TMEM223psi-mi:“MI:0914”(association)0.350
HTR3CTMEM223psi-mi:“MI:0914”(association)0.350
PCDHA4TMEM223psi-mi:“MI:0914”(association)0.350
CHRNA9TMEM120Bpsi-mi:“MI:0914”(association)0.350
TENT5ATMEM131Lpsi-mi:“MI:0914”(association)0.350
NLGN3TMEM131Lpsi-mi:“MI:0914”(association)0.350
SLC39A12POM121Cpsi-mi:“MI:0914”(association)0.350
TMPRSS3UPK3BL1psi-mi:“MI:0914”(association)0.350
CDH5ARVCFpsi-mi:“MI:0914”(association)0.350
IL17RCC2CD2Lpsi-mi:“MI:0914”(association)0.350
MPPE1ADAM10psi-mi:“MI:0914”(association)0.350
PCDHGA5MAP2K7psi-mi:“MI:0914”(association)0.350

BioGRID (75): TMEM39A (Affinity Capture-MS), TMEM39A (Affinity Capture-MS), TMEM39A (Affinity Capture-MS), TMEM39A (Affinity Capture-MS), TMEM39A (Affinity Capture-MS), TMEM39A (Affinity Capture-MS), TMEM39A (Affinity Capture-MS), TMEM39A (Affinity Capture-MS), TMEM39A (Affinity Capture-MS), TMEM39A (Affinity Capture-MS), TMEM39A (Affinity Capture-MS), TMEM39A (Affinity Capture-MS), TMEM39A (Affinity Capture-MS), TMEM39A (Affinity Capture-MS), TMEM39A (Affinity Capture-MS)

ESM2 similar proteins: A0A8I3MKU8, A9RA88, B0CMA4, B3M3X7, B3NGS7, B4GZN1, B4HEB1, B4J2W3, B4L184, B4LC58, B4N5D3, B4PF15, B4QPR1, F4K2U8, I6VSD2, Q0V947, Q12016, Q1DKX4, Q28FG4, Q28FY5, Q2LZ37, Q2TA63, Q3SZR6, Q5F3W2, Q5FWK6, Q5FWM8, Q5R687, Q5R9R3, Q5T9L3, Q5U4Q2, Q5ZLR1, Q66IZ4, Q66J27, Q6DFI2, Q6DGL7, Q6DID7, Q6P689, Q6PQZ3, Q7SY10, Q80UA9

Diamond homologs: Q0IHF1, Q0VCF5, Q17QW2, Q5U2V9, Q66H44, Q6DF19, Q6GL42, Q6GNY8, Q6NRI4, Q6PH58, Q7ZW11, Q810L4, Q9CYC3, Q9GZU3, Q9NV64

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 75 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
Neurotransmitter receptors and postsynaptic signal transmission714.6×4e-05
Transmission across Chemical Synapses711.1×1e-04
Neuronal System98.3×8e-05

GO biological processes:

GO termPartnersFoldFDR
monoatomic ion transmembrane transport929.7×8e-09

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance44
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2193 predictions. Top by Δscore:

VariantEffectΔscore
3:119436789:A:ACdonor_gain1.0000
3:119436790:C:CCdonor_gain1.0000
3:119436977:CT:Cacceptor_gain1.0000
3:119437750:CTTA:Cdonor_loss1.0000
3:119437751:TTA:Tdonor_loss1.0000
3:119437752:TACCT:Tdonor_loss1.0000
3:119437753:ACCT:Adonor_loss1.0000
3:119437754:C:CAdonor_loss1.0000
3:119437819:T:TAdonor_gain1.0000
3:119432215:C:CCacceptor_gain0.9900
3:119436785:A:ACdonor_gain0.9900
3:119436786:C:CCdonor_gain0.9900
3:119436786:CTCA:Cdonor_gain0.9900
3:119436790:CAT:Cdonor_gain0.9900
3:119436975:TACT:Tacceptor_gain0.9900
3:119436979:C:CCacceptor_gain0.9900
3:119436990:C:CTacceptor_gain0.9900
3:119437591:T:Cdonor_gain0.9900
3:119437753:A:ACdonor_gain0.9900
3:119437754:C:CCdonor_gain0.9900
3:119437754:CCTT:Cdonor_gain0.9900
3:119438002:T:Adonor_gain0.9900
3:119438099:CAAAC:Cacceptor_gain0.9900
3:119438101:AACC:Aacceptor_loss0.9900
3:119438102:ACCT:Aacceptor_loss0.9900
3:119438104:C:CCacceptor_gain0.9900
3:119438226:A:Cdonor_gain0.9900
3:119452529:TT:Tacceptor_gain0.9900
3:119452531:C:CCacceptor_gain0.9900
3:119458013:CTTA:Cdonor_loss0.9900

AlphaMissense

3172 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:119432113:C:AW445C1.000
3:119432113:C:GW445C1.000
3:119432115:A:GW445R1.000
3:119432115:A:TW445R1.000
3:119432206:A:CF414L1.000
3:119432206:A:TF414L1.000
3:119432208:A:GF414L1.000
3:119434790:G:CP402R1.000
3:119434790:G:TP402H1.000
3:119434791:G:AP402S1.000
3:119434791:G:TP402T1.000
3:119434801:G:CN398K1.000
3:119434801:G:TN398K1.000
3:119434824:A:CY391D1.000
3:119434861:C:AW378C1.000
3:119434861:C:GW378C1.000
3:119434863:A:GW378R1.000
3:119434863:A:TW378R1.000
3:119434879:C:AW372C1.000
3:119434879:C:GW372C1.000
3:119434881:A:GW372R1.000
3:119434881:A:TW372R1.000
3:119436835:C:AW356C1.000
3:119436835:C:GW356C1.000
3:119436836:C:GW356S1.000
3:119436837:A:GW356R1.000
3:119436837:A:TW356R1.000
3:119436842:C:AG354V1.000
3:119436842:C:TG354D1.000
3:119436843:C:AG354C1.000

dbSNP variants (sampled 300 via entrez): RS1000000439 (3:119434141 G>A), RS1000101276 (3:119455342 CAT>C), RS1000109190 (3:119461908 A>T), RS1000165201 (3:119458635 C>T), RS1000246337 (3:119458564 AG>A), RS1000359203 (3:119464749 A>G), RS1000677429 (3:119445164 C>T), RS1000696652 (3:119452272 G>C), RS1000772710 (3:119464556 C>A), RS1000825077 (3:119445802 G>A), RS1001098368 (3:119432794 T>C), RS1001195358 (3:119465132 C>G), RS1001364382 (3:119441265 A>G), RS1001542929 (3:119446651 A>G), RS1001566953 (3:119452990 T>C)

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

5 associations (top):

StudyTraitp-value
GCST001198_7Multiple sclerosis3.000000e-09
GCST002449_2Plasma omega-6 polyunsaturated fatty acid levels (arachidonic acid)3.000000e-08
GCST003129_25Primary biliary cholangitis4.000000e-15
GCST005581_44Primary biliary cirrhosis7.000000e-16
GCST005752_152Systemic lupus erythematosus1.000000e-11

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0005680omega-6 polyunsaturated fatty acid measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Cyclosporineincreases expression4
sodium arsenitedecreases expression, increases expression3
Valproic Acidaffects expression, decreases expression3
Tobacco Smoke Pollutionincreases expression2
methylmercuric chlorideincreases expression1
beta-lapachoneincreases expression1
didecyldimethylammoniumincreases expression1
potassium chromate(VI)increases expression1
perfluorooctane sulfonic acidincreases expression1
pentabromodiphenyl etherincreases expression1
K 7174increases expression1
pinostrobinincreases phosphorylation1
ICG 001decreases expression1
abrineincreases expression1
2,2’,4,4’-tetrabromodiphenyl etherincreases expression1
NSC 689534affects binding, increases expression1
Air Pollutantsincreases abundance, increases expression1
Air Pollutants, Occupationalaffects expression1
Atrazineincreases expression1
Benzeneincreases expression1
Copperaffects binding, increases expression1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Diurondecreases expression1
Doxorubicindecreases expression1
Dihydrotestosteroneincreases expression1
Sulindacincreases expression1
Testosteronedecreases expression1
Dronabinoldecreases expression1
Thiramincreases expression1
Tunicamycinincreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): primary biliary cholangitis