LTAP1
gene geneOn this page
Also known as NICE-3DKFZp586G1722
Summary
LTAP1 (lipid transport auxiliary protein 1, HGNC:29876) is a protein-coding gene on chromosome 1q21.3, encoding Lipid transport auxiliary protein 1 (Q9BWL3). Required for the formation of endoplasmic reticulum-plasma membrane junctions and functions as an accessory protein for bridge-like lipid transfer protein BLTP1, participating in lipid delivery between endoplasmic reticulum and cell membranes.
Involved in phagocytosis. Located in Golgi apparatus; cytosol; and mitochondrion.
Source: NCBI Gene 25912 — RefSeq curated summary.
At a glance
- GWAS associations: 9
- Clinical variants (ClinVar): 23 total — 1 pathogenic
- MANE Select transcript:
NM_001098616
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:29876 |
| Approved symbol | LTAP1 |
| Name | lipid transport auxiliary protein 1 |
| Location | 1q21.3 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | NICE-3, DKFZp586G1722 |
| Ensembl gene | ENSG00000143612 |
| Ensembl biotype | protein_coding |
| OMIM | 617428 |
| Entrez | 25912 |
Gene structure
Transcript identifiers
Ensembl transcripts: 18 — 14 protein_coding, 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined
ENST00000350592, ENST00000362076, ENST00000368516, ENST00000368518, ENST00000368519, ENST00000368521, ENST00000470180, ENST00000483282, ENST00000493814, ENST00000640799, ENST00000648267, ENST00000882189, ENST00000882190, ENST00000882191, ENST00000882192, ENST00000940679, ENST00000940680, ENST00000958841
RefSeq mRNA: 8 — MANE Select: NM_001098616
NM_001098616, NM_001297717, NM_001297718, NM_001297720, NM_001297721, NM_001297723, NM_015449, NM_138740
CCDS: CCDS1061, CCDS1062, CCDS41404, CCDS72924, CCDS76219, CCDS76220
Canonical transcript exons
ENST00000368521 — 7 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000961109 | 154219836 | 154219937 |
| ENSE00000961110 | 154214457 | 154214574 |
| ENSE00000961112 | 154212458 | 154212624 |
| ENSE00001284813 | 154206720 | 154207648 |
| ENSE00001915171 | 154220342 | 154220590 |
| ENSE00003502774 | 154213893 | 154213946 |
| ENSE00003685514 | 154212320 | 154212378 |
Expression profiles
Bgee: expression breadth ubiquitous, 256 present calls, max score 99.77.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 116.8835 / max 619.8655, expressed in 1827 samples.
FANTOM5 promoters (3 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 14793 | 103.9375 | 1827 |
| 14794 | 11.6835 | 1797 |
| 14795 | 1.2625 | 787 |
Top tissues by expression
256 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| kidney epithelium | UBERON:0004819 | 99.77 | gold quality |
| left ventricle myocardium | UBERON:0006566 | 99.77 | gold quality |
| cardiac muscle of right atrium | UBERON:0003379 | 99.69 | gold quality |
| tibialis anterior | UBERON:0001385 | 99.67 | gold quality |
| ileal mucosa | UBERON:0000331 | 99.61 | gold quality |
| deltoid | UBERON:0001476 | 99.61 | gold quality |
| quadriceps femoris | UBERON:0001377 | 99.57 | gold quality |
| vastus lateralis | UBERON:0001379 | 99.56 | gold quality |
| myocardium | UBERON:0002349 | 99.56 | gold quality |
| skeletal muscle tissue of biceps brachii | UBERON:0004502 | 99.52 | gold quality |
| biceps brachii | UBERON:0001507 | 99.48 | gold quality |
| upper arm skin | UBERON:0004263 | 99.40 | gold quality |
| heart right ventricle | UBERON:0002080 | 99.28 | gold quality |
| Brodmann (1909) area 46 | UBERON:0006483 | 99.28 | gold quality |
| skeletal muscle tissue of rectus abdominis | UBERON:0004511 | 99.27 | gold quality |
| skeletal muscle tissue | UBERON:0001134 | 99.17 | gold quality |
| adult organism | UBERON:0007023 | 99.15 | gold quality |
| jejunal mucosa | UBERON:0000399 | 99.10 | gold quality |
| nasal cavity epithelium | UBERON:0005384 | 99.06 | gold quality |
| body of tongue | UBERON:0011876 | 99.06 | gold quality |
| palpebral conjunctiva | UBERON:0001812 | 99.05 | gold quality |
| muscle tissue | UBERON:0002385 | 99.03 | gold quality |
| pons | UBERON:0000988 | 99.02 | gold quality |
| jejunum | UBERON:0002115 | 99.02 | gold quality |
| bronchial epithelial cell | CL:0002328 | 99.01 | gold quality |
| bronchus | UBERON:0002185 | 98.98 | gold quality |
| caput epididymis | UBERON:0004358 | 98.98 | gold quality |
| corpus epididymis | UBERON:0004359 | 98.97 | gold quality |
| epithelial cell of pancreas | CL:0000083 | 98.96 | gold quality |
| cartilage tissue | UBERON:0002418 | 98.96 | gold quality |
Single-cell (SCXA)
Detected in 2 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-GEOD-125970 | no | 3.25 |
| E-ANND-3 | no | 0.00 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
40 targeting LTAP1, 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-5692A | 100.00 | 74.40 | 6850 |
| HSA-MIR-432-3P | 100.00 | 67.86 | 705 |
| HSA-MIR-340-5P | 100.00 | 72.50 | 4437 |
| HSA-MIR-3667-3P | 99.99 | 67.17 | 1636 |
| HSA-MIR-3658 | 99.96 | 73.87 | 4379 |
| HSA-MIR-1250-3P | 99.96 | 70.04 | 4038 |
| HSA-MIR-2110 | 99.96 | 66.68 | 1930 |
| HSA-MIR-153-5P | 99.89 | 73.86 | 6317 |
| HSA-MIR-9902 | 99.89 | 69.15 | 2250 |
| HSA-MIR-204-5P | 99.79 | 71.62 | 2439 |
| HSA-MIR-211-5P | 99.79 | 71.65 | 2440 |
| HSA-MIR-6505-5P | 99.73 | 69.25 | 1595 |
| HSA-MIR-1825 | 99.72 | 68.11 | 1089 |
| HSA-MIR-494-3P | 99.70 | 71.45 | 2795 |
| HSA-MIR-3202 | 99.66 | 67.70 | 2737 |
| HSA-MIR-6832-3P | 99.52 | 70.44 | 1726 |
| HSA-MIR-12123 | 99.52 | 71.79 | 2990 |
| HSA-MIR-6081 | 99.48 | 66.07 | 1446 |
| HSA-MIR-1275 | 99.47 | 67.90 | 2749 |
| HSA-MIR-3911 | 99.38 | 66.95 | 1087 |
| HSA-MIR-6853-3P | 99.36 | 70.79 | 1558 |
| HSA-MIR-625-5P | 99.02 | 68.64 | 2031 |
| HSA-MIR-4699-5P | 98.99 | 67.50 | 1210 |
| HSA-MIR-29B-1-5P | 98.86 | 68.35 | 1364 |
| HSA-MIR-4477A | 98.83 | 69.75 | 2952 |
| HSA-MIR-502-5P | 98.77 | 66.51 | 906 |
| HSA-MIR-4662A-5P | 98.48 | 67.18 | 1007 |
| HSA-MIR-619-3P | 98.38 | 65.58 | 693 |
| HSA-MIR-18B-3P | 98.05 | 65.55 | 595 |
| HSA-MIR-637 | 97.91 | 64.05 | 1517 |
Literature-anchored findings (GeneRIF, showing 1)
- our findings indicate that NICE-3 may contribute to human hepatocellular carcinoma by promoting cell proliferation. (PMID:23167344)
Cross-species orthologs
6 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | C16H1orf43 | ENSDARG00000055613 |
| ENSDARG00000116978 | ||
| mus_musculus | 4933434E20Rik | ENSMUSG00000027942 |
| rattus_norvegicus | Ns5atp4 | ENSRNOG00000017758 |
| rattus_norvegicus | Ns5atp4-ps3 | ENSRNOG00000027533 |
| drosophila_melanogaster | CG6665 | FBGN0034172 |
Protein
Protein identifiers
Lipid transport auxiliary protein 1 — Q9BWL3 (reviewed: Q9BWL3)
Alternative names: Hepatitis C virus NS5A-transactivated protein 4, Protein NICE-3, S863-3, Spigot ortholog
All UniProt accessions (7): Q9BWL3, A0A1W2PQP6, A0A1W2PQS0, A0A3B3IS96, Q09GN0, X6R6F3, X6R6S3
UniProt curated annotations — full annotation on UniProt →
Function. Required for the formation of endoplasmic reticulum-plasma membrane junctions and functions as an accessory protein for bridge-like lipid transfer protein BLTP1, participating in lipid delivery between endoplasmic reticulum and cell membranes. Regulates the phagocytosis of Gram-negative bacteria like L. pneumophila and E. coli, as well as Gram-positive bacteria such as S. aureus.
Subunit / interactions. Interacts with BLTP1 (via the N-terminus); the interaction is direct.
Subcellular location. Cell membrane. Golgi apparatus. Mitochondrion. Endoplasmic reticulum membrane.
Domain organisation. N-terminal region is required for phagocytosis of Gram negative bacterium.
Similarity. Belongs to the lipid transport auxiliary protein 1 family.
Isoforms (5)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q9BWL3-1 | 1 | yes |
| Q9BWL3-2 | 2, Nice-3 | |
| Q9BWL3-3 | 3 | |
| Q9BWL3-4 | 4 | |
| Q9BWL3-5 | 5 |
RefSeq proteins (8): NP_001092086, NP_001284646, NP_001284647, NP_001284649, NP_001284650, NP_001284652, NP_056264, NP_620077 (=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR010876 | LTAP1 | Family |
Pfam: PF07406
UniProt features (10 total): splice variant 5, topological domain 2, chain 1, transmembrane region 1, sequence conflict 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9BWL3-F1 | 73.35 | 0.27 |
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 164 (showing top):
FREAC2_01, HNF3ALPHA_Q6, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, GOBP_VESICLE_MEDIATED_TRANSPORT, FOXO4_01, FOXO1_01, GGGTGGRR_PAX4_03, PATIL_LIVER_CANCER, MODULE_239, USF_01, WTGAAAT_UNKNOWN, FOXJ2_01, HFH3_01, TGACATY_UNKNOWN, P300_01
GO Biological Process (2): in utero embryonic development (GO:0001701), phagocytosis (GO:0006909)
GO Molecular Function (0):
GO Cellular Component (5): mitochondrion (GO:0005739), Golgi apparatus (GO:0005794), cytosol (GO:0005829), membrane (GO:0016020), endoplasmic reticulum-plasma membrane contact site (GO:0140268)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cytoplasm | 3 |
| intracellular membrane-bounded organelle | 2 |
| cellular anatomical structure | 2 |
| chordate embryonic development | 1 |
| endocytosis | 1 |
| endomembrane system | 1 |
| organelle membrane contact site | 1 |
Protein interactions and networks
STRING
488 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| LTAP1 | EMC7 | Q9NPA0 | 818 |
| LTAP1 | CRCT1 | Q9UGL9 | 657 |
| LTAP1 | CHMP2A | O43633 | 637 |
| LTAP1 | PSMB4 | P28070 | 606 |
| LTAP1 | S100A7A | Q86SG5 | 581 |
| LTAP1 | PSMB2 | P31145 | 538 |
| LTAP1 | VPS29 | Q9UBQ0 | 490 |
| LTAP1 | OR2T5 | Q6IEZ7 | 447 |
| LTAP1 | REEP5 | Q00765 | 439 |
| LTAP1 | RAB7A | P51149 | 423 |
| LTAP1 | CNTN3 | Q9P232 | 415 |
| LTAP1 | VCP | P55072 | 414 |
| LTAP1 | CFAP141 | Q5VU69 | 406 |
| LTAP1 | EMC2 | Q15006 | 404 |
| LTAP1 | CABP2 | Q9NPB3 | 379 |
IntAct
65 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| ENTREP1 | WWP2 | psi-mi:“MI:0914”(association) | 0.850 |
| CFTR | ESYT2 | psi-mi:“MI:2364”(proximity) | 0.710 |
| ADCY9 | NEMP1 | psi-mi:“MI:0914”(association) | 0.640 |
| KCNA5 | TMEM223 | psi-mi:“MI:0914”(association) | 0.530 |
| CXCR4 | TMEM120B | psi-mi:“MI:0914”(association) | 0.530 |
| SLC39A4 | TMEM120B | psi-mi:“MI:0914”(association) | 0.530 |
| BTNL3 | FAM171A2 | psi-mi:“MI:0914”(association) | 0.530 |
| KCNS3 | UPK3BL1 | psi-mi:“MI:0914”(association) | 0.530 |
| LRRTM1 | UPK3BL1 | psi-mi:“MI:0914”(association) | 0.530 |
| ZNRF4 | UPK3BL1 | psi-mi:“MI:0914”(association) | 0.530 |
| MRAP2 | GOLIM4 | psi-mi:“MI:0914”(association) | 0.530 |
| GDPD5 | GOLIM4 | psi-mi:“MI:0914”(association) | 0.530 |
| CNGA3 | C2CD2L | psi-mi:“MI:0914”(association) | 0.530 |
| PCDHB7 | C2CD2L | psi-mi:“MI:0914”(association) | 0.530 |
| KCNA10 | GAPDHS | psi-mi:“MI:0914”(association) | 0.530 |
| CHRNA9 | CHEK1 | psi-mi:“MI:0914”(association) | 0.530 |
| TEX264 | PER1 | psi-mi:“MI:0914”(association) | 0.530 |
| CHRND | TPST2 | psi-mi:“MI:0914”(association) | 0.530 |
| KCNJ6 | MB21D2 | psi-mi:“MI:0914”(association) | 0.530 |
| C1orf43 | BDKRB1 | psi-mi:“MI:0915”(physical association) | 0.370 |
| incE | STX7 | psi-mi:“MI:0914”(association) | 0.350 |
| KCNA2 | TMEM129 | psi-mi:“MI:0914”(association) | 0.350 |
| TTMP | TMEM223 | psi-mi:“MI:0914”(association) | 0.350 |
| TTYH1 | TMEM223 | psi-mi:“MI:0914”(association) | 0.350 |
| CHRNA4 | TMEM223 | psi-mi:“MI:0914”(association) | 0.350 |
| OR1M1 | NBAS | psi-mi:“MI:0914”(association) | 0.350 |
| ZDHHC12 | NBAS | psi-mi:“MI:0914”(association) | 0.350 |
| IL17RC | TMEM131L | psi-mi:“MI:0914”(association) | 0.350 |
| PDE3A | TMEM131L | psi-mi:“MI:0914”(association) | 0.350 |
| SIDT2 | KLRG2 | psi-mi:“MI:0914”(association) | 0.350 |
BioGRID (135): C1orf43 (Affinity Capture-RNA), C1orf43 (Affinity Capture-RNA), C1orf43 (Affinity Capture-MS), C1orf43 (Affinity Capture-MS), C1orf43 (Affinity Capture-MS), C1orf43 (Affinity Capture-MS), C1orf43 (Affinity Capture-MS), C1orf43 (Affinity Capture-MS), C1orf43 (Affinity Capture-MS), C1orf43 (Affinity Capture-MS), C1orf43 (Affinity Capture-MS), C1orf43 (Affinity Capture-MS), C1orf43 (Affinity Capture-MS), C1orf43 (Affinity Capture-MS), C1orf43 (Affinity Capture-MS)
ESM2 similar proteins: A0A1B0GVV1, A0M8S0, A0M8T1, A0M8U1, A3KN28, A4D7R9, A9JRA0, B1AZA5, E9Q2Z6, P01134, P48030, Q00PJ0, Q07DV5, Q07DW9, Q07DX8, Q07DY8, Q07E08, Q07E45, Q09YH4, Q09YI5, Q09YJ7, Q09YK8, Q09YN2, Q108U3, Q1RLU8, Q2IBA8, Q2IBD0, Q2IBE0, Q2IBE8, Q2PG42, Q2QL86, Q2QLA6, Q2QLB7, Q2QLD7, Q2QLE8, Q2QLG2, Q3KRC4, Q3SXP7, Q5T292, Q68FW3
Diamond homologs: Q5E943, Q5RF08, Q5XII8, Q8R092, Q9BWL3
SIGNOR signaling
0 interactions.
Enriched among interaction partners
Reactome pathways and GO biological processes over-represented among this gene’s 95 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 | 12.5× | 2e-04 |
| Potassium Channels | 5 | 12.0× | 1e-03 |
| Transmission across Chemical Synapses | 7 | 9.5× | 4e-04 |
| Neuronal System | 12 | 9.5× | 8e-07 |
| Transport of small molecules | 9 | 4.0× | 4e-03 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| action potential | 5 | 23.0× | 5e-04 |
| regulation of membrane potential | 7 | 20.7× | 2e-05 |
| potassium ion transport | 6 | 14.7× | 5e-04 |
| monoatomic ion transmembrane transport | 5 | 13.3× | 2e-03 |
| protein homooligomerization | 6 | 9.4× | 2e-03 |
| potassium ion transmembrane transport | 5 | 8.7× | 6e-03 |
| positive regulation of cytosolic calcium ion concentration | 5 | 7.5× | 1e-02 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
23 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 1 |
| Likely pathogenic | 0 |
| Uncertain significance | 1 |
| Likely benign | 0 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (1)
| Variant ID | HGVS | Classification |
|---|---|---|
| 60011 | GRCh38/hg38 1q21.3(chr1:153759563-154219803)x1 | Pathogenic |
SpliceAI
941 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 1:154207647:CC:C | acceptor_gain | 1.0000 |
| 1:154207648:CC:C | acceptor_gain | 1.0000 |
| 1:154212452:GCTTA:G | donor_loss | 1.0000 |
| 1:154212453:CTTA:C | donor_loss | 1.0000 |
| 1:154212454:TTACC:T | donor_loss | 1.0000 |
| 1:154212455:TACC:T | donor_loss | 1.0000 |
| 1:154212456:ACC:A | donor_gain | 1.0000 |
| 1:154212456:ACCCC:A | donor_loss | 1.0000 |
| 1:154212457:CCC:C | donor_gain | 1.0000 |
| 1:154212519:ACAC:A | donor_gain | 1.0000 |
| 1:154212520:CACC:C | donor_gain | 1.0000 |
| 1:154212620:GATCT:G | acceptor_gain | 1.0000 |
| 1:154212621:ATCT:A | acceptor_gain | 1.0000 |
| 1:154212623:CT:C | acceptor_gain | 1.0000 |
| 1:154212624:TCTGT:T | acceptor_loss | 1.0000 |
| 1:154212625:C:CC | acceptor_gain | 1.0000 |
| 1:154212626:T:G | acceptor_loss | 1.0000 |
| 1:154214427:A:AC | donor_gain | 1.0000 |
| 1:154214428:C:CC | donor_gain | 1.0000 |
| 1:154214453:ATAC:A | donor_loss | 1.0000 |
| 1:154214454:TACT:T | donor_loss | 1.0000 |
| 1:154214455:A:AC | donor_gain | 1.0000 |
| 1:154214455:A:AT | donor_loss | 1.0000 |
| 1:154214456:C:CG | donor_loss | 1.0000 |
| 1:154214456:C:CT | donor_gain | 1.0000 |
| 1:154214456:CT:C | donor_gain | 1.0000 |
| 1:154214465:C:A | donor_gain | 1.0000 |
| 1:154214583:A:C | acceptor_gain | 1.0000 |
| 1:154207644:TAACC:T | acceptor_gain | 0.9900 |
| 1:154207645:AACC:A | acceptor_gain | 0.9900 |
AlphaMissense
1649 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 1:154219905:C:A | R33S | 1.000 |
| 1:154219905:C:G | R33S | 1.000 |
| 1:154219906:C:A | R33M | 1.000 |
| 1:154219906:C:G | R33T | 1.000 |
| 1:154220345:G:C | S21R | 1.000 |
| 1:154220345:G:T | S21R | 1.000 |
| 1:154220347:T:G | S21R | 1.000 |
| 1:154220349:C:T | G20E | 1.000 |
| 1:154220350:C:G | G20R | 1.000 |
| 1:154220350:C:T | G20R | 1.000 |
| 1:154207486:C:A | K243N | 0.999 |
| 1:154207486:C:G | K243N | 0.999 |
| 1:154207499:A:G | L239S | 0.999 |
| 1:154212474:G:T | A164D | 0.999 |
| 1:154213924:C:A | R103S | 0.999 |
| 1:154213924:C:G | R103S | 0.999 |
| 1:154213925:C:A | R103M | 0.999 |
| 1:154213925:C:G | R103T | 0.999 |
| 1:154219843:G:T | A54D | 0.999 |
| 1:154219852:C:T | G51E | 0.999 |
| 1:154219853:C:G | G51R | 0.999 |
| 1:154219853:C:T | G51R | 0.999 |
| 1:154219891:A:G | F38S | 0.999 |
| 1:154219895:G:T | R37S | 0.999 |
| 1:154219900:A:C | I35S | 0.999 |
| 1:154219900:A:G | I35T | 0.999 |
| 1:154219900:A:T | I35N | 0.999 |
| 1:154219903:T:G | Q34P | 0.999 |
| 1:154219908:C:A | K32N | 0.999 |
| 1:154219908:C:G | K32N | 0.999 |
dbSNP variants (sampled 300 via entrez): RS1000488447 (1:154208900 A>G), RS1000674737 (1:154208977 A>C), RS1000876453 (1:154207026 A>G), RS1000972075 (1:154212874 T>C), RS1001040845 (1:154218291 A>G,T), RS1001067363 (1:154213513 T>C), RS1001069079 (1:154207362 G>A), RS1001309662 (1:154218503 C>G), RS1001352044 (1:154218385 G>A), RS1001417321 (1:154207659 G>C), RS1002086919 (1:154221013 GGCGGCAGCGGCA>G,GGCGGCAGCGGCAGCGGCA,GGCGGCAGCGGCAGCGGCAGCGGCA), RS1002434522 (1:154213259 A>G), RS1002936747 (1:154210791 A>G), RS1002992267 (1:154216006 T>C), RS1003040598 (1:154210282 G>A,C)
Disease associations
OMIM: gene MIM:617428 | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
9 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST010142_92 | Fish- and plant-related diet | 6.000000e-14 |
| GCST010696_22 | Cortical thickness (min-P) | 4.000000e-10 |
| GCST010697_50 | Cortical surface area (min-P) | 1.000000e-12 |
| GCST010698_81 | Subcortical volume (min-P) | 1.000000e-23 |
| GCST010699_7 | Brain morphology (min-P) | 1.000000e-10 |
| GCST010700_11 | Cortical thickness (MOSTest) | 4.000000e-13 |
| GCST010701_73 | Cortical surface area (MOSTest) | 4.000000e-09 |
| GCST010702_45 | Subcortical volume (MOSTest) | 4.000000e-10 |
| GCST010703_276 | Brain morphology (MOSTest) | 2.000000e-15 |
EFO canonical traits (3, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0008111 | diet measurement |
| EFO:0004346 | neuroimaging measurement |
| EFO:0004840 | cortical thickness |
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 |
|---|---|---|
| Valproic Acid | affects cotreatment, increases expression, affects expression, decreases methylation | 6 |
| aristolochic acid I | increases expression | 1 |
| FR900359 | increases phosphorylation | 1 |
| triphenyl phosphate | affects expression | 1 |
| uranyl acetate | affects expression | 1 |
| bisphenol A | affects expression | 1 |
| trichostatin A | affects expression | 1 |
| beta-lapachone | increases expression | 1 |
| tris(1,3-dichloro-2-propyl)phosphate | increases expression | 1 |
| perfluorooctane sulfonic acid | increases expression | 1 |
| K 7174 | increases expression | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, increases expression | 1 |
| dorsomorphin | affects cotreatment, increases expression | 1 |
| 4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid | decreases expression | 1 |
| Bortezomib | decreases expression | 1 |
| Irinotecan | decreases expression | 1 |
| Sunitinib | increases expression | 1 |
| Cadmium | increases abundance, increases expression | 1 |
| Doxorubicin | increases expression | 1 |
| Gasoline | affects cotreatment, increases abundance, increases expression | 1 |
| Hydrogen Peroxide | decreases expression, affects cotreatment, increases expression | 1 |
| Nickel | increases expression | 1 |
| Polycyclic Aromatic Hydrocarbons | increases abundance, increases expression, affects cotreatment | 1 |
| Smoke | decreases expression | 1 |
| Dronabinol | increases expression | 1 |
| Theophylline | affects cotreatment, increases expression | 1 |
| Thiram | decreases expression | 1 |
| Tobacco Smoke Pollution | increases expression | 1 |
| Uranium | affects expression | 1 |
| Aflatoxin B1 | increases expression | 1 |
Cellosaurus cell lines
5 cell lines: 4 cancer cell line, 1 transformed cell line
First 10 cell lines (id-ordered, not curated):
| Cellosaurus | Name | Category | Sex |
|---|---|---|---|
| CVCL_B2T9 | Abcam HEK293T C1orf43 KO | Transformed cell line | Female |
| CVCL_SG23 | HAP1 C1orf43 (-) 1 | Cancer cell line | Male |
| CVCL_SG24 | HAP1 C1orf43 (-) 2 | Cancer cell line | Male |
| CVCL_SG25 | HAP1 C1orf43 (-) 3 | Cancer cell line | Male |
| CVCL_SG26 | HAP1 C1orf43 (-) 4 | Cancer cell line | Male |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.