TMEM39A
gene geneOn this page
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
| Field | Value |
|---|---|
| HGNC ID | HGNC:25600 |
| Approved symbol | TMEM39A |
| Name | transmembrane protein 39A |
| Location | 3q13.33 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | FLJ10902, SUSR2 |
| Ensembl gene | ENSG00000176142 |
| Ensembl biotype | protein_coding |
| Entrez | 55254 |
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
| Exon | Start | End |
|---|---|---|
| ENSE00001857038 | 119463336 | 119463615 |
| ENSE00003472202 | 119436791 | 119436978 |
| ENSE00003560311 | 119437755 | 119438103 |
| ENSE00003577939 | 119428949 | 119432214 |
| ENSE00003581208 | 119434762 | 119434882 |
| ENSE00003630088 | 119461962 | 119462148 |
| ENSE00003784324 | 119447018 | 119447172 |
| ENSE00003785531 | 119452447 | 119452530 |
| ENSE00003789003 | 119458018 | 119458240 |
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 ID | TPM avg | Samples expressed |
|---|---|---|
| 43983 | 32.7496 | 1813 |
| 43985 | 0.6041 | 276 |
| 43984 | 0.4368 | 193 |
| 43988 | 0.3139 | 99 |
| 43986 | 0.2554 | 49 |
| 43987 | 0.0905 | 30 |
| 43982 | 0.0769 | 27 |
Top tissues by expression
275 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| stromal cell of endometrium | CL:0002255 | 96.33 | gold quality |
| body of pancreas | UBERON:0001150 | 95.82 | gold quality |
| tibia | UBERON:0000979 | 93.51 | gold quality |
| pancreas | UBERON:0001264 | 92.79 | gold quality |
| right lung | UBERON:0002167 | 92.10 | gold quality |
| calcaneal tendon | UBERON:0003701 | 92.07 | gold quality |
| upper lobe of left lung | UBERON:0008952 | 91.79 | gold quality |
| right lobe of thyroid gland | UBERON:0001119 | 91.66 | gold quality |
| left lobe of thyroid gland | UBERON:0001120 | 91.62 | gold quality |
| colonic epithelium | UBERON:0000397 | 91.26 | gold quality |
| cartilage tissue | UBERON:0002418 | 91.26 | gold quality |
| endocervix | UBERON:0000458 | 91.00 | gold quality |
| upper lobe of lung | UBERON:0008948 | 90.99 | gold quality |
| thyroid gland | UBERON:0002046 | 90.78 | gold quality |
| gall bladder | UBERON:0002110 | 90.57 | gold quality |
| tibial nerve | UBERON:0001323 | 90.43 | gold quality |
| adenohypophysis | UBERON:0002196 | 90.39 | gold quality |
| minor salivary gland | UBERON:0001830 | 90.37 | gold quality |
| pituitary gland | UBERON:0000007 | 90.31 | gold quality |
| body of uterus | UBERON:0009853 | 90.19 | gold quality |
| right ovary | UBERON:0002118 | 90.15 | gold quality |
| omental fat pad | UBERON:0010414 | 89.78 | gold quality |
| peritoneum | UBERON:0002358 | 89.76 | gold quality |
| adrenal tissue | UBERON:0018303 | 89.66 | gold quality |
| monocyte | CL:0000576 | 89.62 | gold quality |
| saliva-secreting gland | UBERON:0001044 | 89.60 | gold quality |
| left ovary | UBERON:0002119 | 89.59 | gold quality |
| right atrium auricular region | UBERON:0006631 | 89.53 | gold quality |
| islet of Langerhans | UBERON:0000006 | 89.42 | gold quality |
| mononuclear cell | CL:0000842 | 89.40 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | no | 0.00 |
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):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-3163 | 100.00 | 77.23 | 8605 |
| HSA-MIR-1277-5P | 100.00 | 73.95 | 5056 |
| HSA-MIR-340-5P | 100.00 | 72.50 | 4437 |
| HSA-LET-7A-3P | 100.00 | 74.03 | 3932 |
| HSA-LET-7B-3P | 100.00 | 74.08 | 3913 |
| HSA-LET-7F-1-3P | 100.00 | 74.02 | 3928 |
| HSA-MIR-98-3P | 100.00 | 74.08 | 3907 |
| HSA-MIR-12118 | 100.00 | 65.88 | 1270 |
| HSA-MIR-656-3P | 100.00 | 72.15 | 2788 |
| HSA-MIR-4682 | 100.00 | 68.89 | 1258 |
| HSA-MIR-548C-3P | 99.99 | 74.01 | 7587 |
| HSA-MIR-513B-5P | 99.99 | 69.96 | 2150 |
| HSA-MIR-4789-3P | 99.99 | 70.75 | 2484 |
| HSA-MIR-196A-1-3P | 99.99 | 72.15 | 2772 |
| HSA-MIR-3173-3P | 99.98 | 66.49 | 1217 |
| HSA-MIR-6891-5P | 99.98 | 66.53 | 1372 |
| HSA-MIR-4803 | 99.98 | 71.99 | 3117 |
| HSA-MIR-3692-3P | 99.98 | 70.27 | 2139 |
| HSA-MIR-607 | 99.97 | 73.62 | 5593 |
| HSA-MIR-3065-5P | 99.97 | 71.56 | 3281 |
| HSA-MIR-495-3P | 99.96 | 72.81 | 4197 |
| HSA-MIR-5688 | 99.96 | 73.23 | 4504 |
| HSA-MIR-4666A-3P | 99.96 | 71.71 | 3434 |
| HSA-MIR-570-3P | 99.96 | 72.41 | 4910 |
| HSA-MIR-128-3P | 99.95 | 71.17 | 2484 |
| HSA-MIR-216A-3P | 99.95 | 71.19 | 2505 |
| HSA-MIR-1236-3P | 99.94 | 68.04 | 1695 |
| HSA-MIR-4778-3P | 99.93 | 70.40 | 1818 |
| HSA-MIR-381-3P | 99.93 | 71.87 | 2854 |
| HSA-MIR-1-3P | 99.93 | 72.35 | 1914 |
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
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | tmem39a | ENSDARG00000102746 |
| mus_musculus | Tmem39a | ENSMUSG00000002845 |
| rattus_norvegicus | Tmem39a | ENSRNOG00000003075 |
| drosophila_melanogaster | CG13016 | FBGN0033899 |
| caenorhabditis_elegans | tmem-39 | WBGENE00017003 |
Paralogs (1): TMEM39B (ENSG00000121775)
Protein
Protein identifiers
Transmembrane protein 39A — Q9NV64 (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 ID | Names | Canonical? |
|---|---|---|
| Q9NV64-1 | 1 | yes |
| Q9NV64-2 | 2 |
RefSeq proteins (1): NP_060736* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR019397 | Uncharacterised_TMEM39 | Family |
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)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9NV64-F1 | 74.80 | 0.30 |
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:
| Category | Terms |
|---|---|
| negative regulation of macroautophagy | 2 |
| catabolic process | 1 |
| transmembrane transport | 1 |
| process utilizing autophagic mechanism | 1 |
| viral genome replication | 1 |
| regulation of viral genome replication | 1 |
| positive regulation of viral process | 1 |
| negative regulation of protein-containing complex disassembly | 1 |
| autophagosome maturation | 1 |
| regulation of autophagosome maturation | 1 |
| autophagosome assembly | 1 |
| negative regulation of organelle assembly | 1 |
| regulation of autophagosome assembly | 1 |
| binding | 1 |
| organelle membrane | 1 |
| nuclear outer membrane-endoplasmic reticulum membrane network | 1 |
| endoplasmic reticulum subcompartment | 1 |
| cytoplasm | 1 |
| endomembrane system | 1 |
| intracellular membrane-bounded organelle | 1 |
| cellular anatomical structure | 1 |
Protein interactions and networks
STRING
538 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| TMEM39A | CLEC16A | Q2KHT3 | 527 |
| TMEM39A | ARHGAP31 | Q2M1Z3 | 520 |
| TMEM39A | SEC24B | O95487 | 518 |
| TMEM39A | TIMMDC1 | Q9NPL8 | 507 |
| TMEM39A | CHRNA9 | Q9UGM1 | 466 |
| TMEM39A | KIF21B | O75037 | 442 |
| TMEM39A | IQCJ | Q1A5X6 | 419 |
| TMEM39A | POU2AF2 | Q8IXP5 | 400 |
| TMEM39A | EVI5 | O60447 | 399 |
| TMEM39A | ZPBP2 | Q6X784 | 399 |
| TMEM39A | MACIR | Q96GV9 | 398 |
| TMEM39A | POGLUT1 | Q8NBL1 | 397 |
| TMEM39A | EXOC3L4 | Q17RC7 | 391 |
| TMEM39A | TMEM25 | Q86YD3 | 389 |
| TMEM39A | CFAP263 | Q9H0I3 | 367 |
| TMEM39A | OR8D4 | Q8NGM9 | 367 |
IntAct
64 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| GABRE | FZD6 | psi-mi:“MI:0914”(association) | 0.530 |
| ZNRF4 | UPK3BL1 | psi-mi:“MI:0914”(association) | 0.530 |
| ZACN | GPAA1 | psi-mi:“MI:0914”(association) | 0.530 |
| TCTN2 | TPST2 | psi-mi:“MI:0914”(association) | 0.530 |
| GAA | B3GAT3 | psi-mi:“MI:0914”(association) | 0.530 |
| TM2D2 | TMEM97 | psi-mi:“MI:0914”(association) | 0.530 |
| IL9R | RETSAT | psi-mi:“MI:0914”(association) | 0.530 |
| FBXO2 | TMEM131L | psi-mi:“MI:0914”(association) | 0.530 |
| LRRTM1 | UPK3BL1 | psi-mi:“MI:0914”(association) | 0.530 |
| CHRNA9 | CHEK1 | psi-mi:“MI:0914”(association) | 0.530 |
| B4GAT1 | ADCY6 | psi-mi:“MI:0914”(association) | 0.530 |
| CHRND | TPST2 | psi-mi:“MI:0914”(association) | 0.530 |
| ADAM21 | PLXNA2 | psi-mi:“MI:0914”(association) | 0.530 |
| FKBP2 | TTC13 | psi-mi:“MI:0914”(association) | 0.530 |
| TMEM39A | rep | psi-mi:“MI:0915”(physical association) | 0.370 |
| UPK1A | TMEM223 | psi-mi:“MI:0914”(association) | 0.350 |
| LRRTM1 | TMEM223 | psi-mi:“MI:0914”(association) | 0.350 |
| HTR3C | TMEM223 | psi-mi:“MI:0914”(association) | 0.350 |
| PCDHA4 | TMEM223 | psi-mi:“MI:0914”(association) | 0.350 |
| CHRNA9 | TMEM120B | psi-mi:“MI:0914”(association) | 0.350 |
| TENT5A | TMEM131L | psi-mi:“MI:0914”(association) | 0.350 |
| NLGN3 | TMEM131L | psi-mi:“MI:0914”(association) | 0.350 |
| SLC39A12 | POM121C | psi-mi:“MI:0914”(association) | 0.350 |
| TMPRSS3 | UPK3BL1 | psi-mi:“MI:0914”(association) | 0.350 |
| CDH5 | ARVCF | psi-mi:“MI:0914”(association) | 0.350 |
| IL17RC | C2CD2L | psi-mi:“MI:0914”(association) | 0.350 |
| MPPE1 | ADAM10 | psi-mi:“MI:0914”(association) | 0.350 |
| PCDHGA5 | MAP2K7 | psi-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:
| Pathway | Partners | Fold | FDR |
|---|---|---|---|
| Neurotransmitter receptors and postsynaptic signal transmission | 7 | 14.6× | 4e-05 |
| Transmission across Chemical Synapses | 7 | 11.1× | 1e-04 |
| Neuronal System | 9 | 8.3× | 8e-05 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| monoatomic ion transmembrane transport | 9 | 29.7× | 8e-09 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
55 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 44 |
| Likely benign | 0 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
2193 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 3:119436789:A:AC | donor_gain | 1.0000 |
| 3:119436790:C:CC | donor_gain | 1.0000 |
| 3:119436977:CT:C | acceptor_gain | 1.0000 |
| 3:119437750:CTTA:C | donor_loss | 1.0000 |
| 3:119437751:TTA:T | donor_loss | 1.0000 |
| 3:119437752:TACCT:T | donor_loss | 1.0000 |
| 3:119437753:ACCT:A | donor_loss | 1.0000 |
| 3:119437754:C:CA | donor_loss | 1.0000 |
| 3:119437819:T:TA | donor_gain | 1.0000 |
| 3:119432215:C:CC | acceptor_gain | 0.9900 |
| 3:119436785:A:AC | donor_gain | 0.9900 |
| 3:119436786:C:CC | donor_gain | 0.9900 |
| 3:119436786:CTCA:C | donor_gain | 0.9900 |
| 3:119436790:CAT:C | donor_gain | 0.9900 |
| 3:119436975:TACT:T | acceptor_gain | 0.9900 |
| 3:119436979:C:CC | acceptor_gain | 0.9900 |
| 3:119436990:C:CT | acceptor_gain | 0.9900 |
| 3:119437591:T:C | donor_gain | 0.9900 |
| 3:119437753:A:AC | donor_gain | 0.9900 |
| 3:119437754:C:CC | donor_gain | 0.9900 |
| 3:119437754:CCTT:C | donor_gain | 0.9900 |
| 3:119438002:T:A | donor_gain | 0.9900 |
| 3:119438099:CAAAC:C | acceptor_gain | 0.9900 |
| 3:119438101:AACC:A | acceptor_loss | 0.9900 |
| 3:119438102:ACCT:A | acceptor_loss | 0.9900 |
| 3:119438104:C:CC | acceptor_gain | 0.9900 |
| 3:119438226:A:C | donor_gain | 0.9900 |
| 3:119452529:TT:T | acceptor_gain | 0.9900 |
| 3:119452531:C:CC | acceptor_gain | 0.9900 |
| 3:119458013:CTTA:C | donor_loss | 0.9900 |
AlphaMissense
3172 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 3:119432113:C:A | W445C | 1.000 |
| 3:119432113:C:G | W445C | 1.000 |
| 3:119432115:A:G | W445R | 1.000 |
| 3:119432115:A:T | W445R | 1.000 |
| 3:119432206:A:C | F414L | 1.000 |
| 3:119432206:A:T | F414L | 1.000 |
| 3:119432208:A:G | F414L | 1.000 |
| 3:119434790:G:C | P402R | 1.000 |
| 3:119434790:G:T | P402H | 1.000 |
| 3:119434791:G:A | P402S | 1.000 |
| 3:119434791:G:T | P402T | 1.000 |
| 3:119434801:G:C | N398K | 1.000 |
| 3:119434801:G:T | N398K | 1.000 |
| 3:119434824:A:C | Y391D | 1.000 |
| 3:119434861:C:A | W378C | 1.000 |
| 3:119434861:C:G | W378C | 1.000 |
| 3:119434863:A:G | W378R | 1.000 |
| 3:119434863:A:T | W378R | 1.000 |
| 3:119434879:C:A | W372C | 1.000 |
| 3:119434879:C:G | W372C | 1.000 |
| 3:119434881:A:G | W372R | 1.000 |
| 3:119434881:A:T | W372R | 1.000 |
| 3:119436835:C:A | W356C | 1.000 |
| 3:119436835:C:G | W356C | 1.000 |
| 3:119436836:C:G | W356S | 1.000 |
| 3:119436837:A:G | W356R | 1.000 |
| 3:119436837:A:T | W356R | 1.000 |
| 3:119436842:C:A | G354V | 1.000 |
| 3:119436842:C:T | G354D | 1.000 |
| 3:119436843:C:A | G354C | 1.000 |
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):
| Study | Trait | p-value |
|---|---|---|
| GCST001198_7 | Multiple sclerosis | 3.000000e-09 |
| GCST002449_2 | Plasma omega-6 polyunsaturated fatty acid levels (arachidonic acid) | 3.000000e-08 |
| GCST003129_25 | Primary biliary cholangitis | 4.000000e-15 |
| GCST005581_44 | Primary biliary cirrhosis | 7.000000e-16 |
| GCST005752_152 | Systemic lupus erythematosus | 1.000000e-11 |
EFO canonical traits (1, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0005680 | omega-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.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Cyclosporine | increases expression | 4 |
| sodium arsenite | decreases expression, increases expression | 3 |
| Valproic Acid | affects expression, decreases expression | 3 |
| Tobacco Smoke Pollution | increases expression | 2 |
| methylmercuric chloride | increases expression | 1 |
| beta-lapachone | increases expression | 1 |
| didecyldimethylammonium | increases expression | 1 |
| potassium chromate(VI) | increases expression | 1 |
| perfluorooctane sulfonic acid | increases expression | 1 |
| pentabromodiphenyl ether | increases expression | 1 |
| K 7174 | increases expression | 1 |
| pinostrobin | increases phosphorylation | 1 |
| ICG 001 | decreases expression | 1 |
| abrine | increases expression | 1 |
| 2,2’,4,4’-tetrabromodiphenyl ether | increases expression | 1 |
| NSC 689534 | affects binding, increases expression | 1 |
| Air Pollutants | increases abundance, increases expression | 1 |
| Air Pollutants, Occupational | affects expression | 1 |
| Atrazine | increases expression | 1 |
| Benzene | increases expression | 1 |
| Copper | affects binding, increases expression | 1 |
| Dichlorodiphenyl Dichloroethylene | decreases expression | 1 |
| Diuron | decreases expression | 1 |
| Doxorubicin | decreases expression | 1 |
| Dihydrotestosterone | increases expression | 1 |
| Sulindac | increases expression | 1 |
| Testosterone | decreases expression | 1 |
| Dronabinol | decreases expression | 1 |
| Thiram | increases expression | 1 |
| Tunicamycin | increases expression | 1 |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): primary biliary cholangitis