LTAP1

gene
On 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

FieldValue
HGNC IDHGNC:29876
Approved symbolLTAP1
Namelipid transport auxiliary protein 1
Location1q21.3
Locus typegene with protein product
StatusApproved
AliasesNICE-3, DKFZp586G1722
Ensembl geneENSG00000143612
Ensembl biotypeprotein_coding
OMIM617428
Entrez25912

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

ExonStartEnd
ENSE00000961109154219836154219937
ENSE00000961110154214457154214574
ENSE00000961112154212458154212624
ENSE00001284813154206720154207648
ENSE00001915171154220342154220590
ENSE00003502774154213893154213946
ENSE00003685514154212320154212378

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 IDTPM avgSamples expressed
14793103.93751827
1479411.68351797
147951.2625787

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
kidney epitheliumUBERON:000481999.77gold quality
left ventricle myocardiumUBERON:000656699.77gold quality
cardiac muscle of right atriumUBERON:000337999.69gold quality
tibialis anteriorUBERON:000138599.67gold quality
ileal mucosaUBERON:000033199.61gold quality
deltoidUBERON:000147699.61gold quality
quadriceps femorisUBERON:000137799.57gold quality
vastus lateralisUBERON:000137999.56gold quality
myocardiumUBERON:000234999.56gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450299.52gold quality
biceps brachiiUBERON:000150799.48gold quality
upper arm skinUBERON:000426399.40gold quality
heart right ventricleUBERON:000208099.28gold quality
Brodmann (1909) area 46UBERON:000648399.28gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451199.27gold quality
skeletal muscle tissueUBERON:000113499.17gold quality
adult organismUBERON:000702399.15gold quality
jejunal mucosaUBERON:000039999.10gold quality
nasal cavity epitheliumUBERON:000538499.06gold quality
body of tongueUBERON:001187699.06gold quality
palpebral conjunctivaUBERON:000181299.05gold quality
muscle tissueUBERON:000238599.03gold quality
ponsUBERON:000098899.02gold quality
jejunumUBERON:000211599.02gold quality
bronchial epithelial cellCL:000232899.01gold quality
bronchusUBERON:000218598.98gold quality
caput epididymisUBERON:000435898.98gold quality
corpus epididymisUBERON:000435998.97gold quality
epithelial cell of pancreasCL:000008398.96gold quality
cartilage tissueUBERON:000241898.96gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-GEOD-125970no3.25
E-ANND-3no0.00

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):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-5692A100.0074.406850
HSA-MIR-432-3P100.0067.86705
HSA-MIR-340-5P100.0072.504437
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-365899.9673.874379
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-211099.9666.681930
HSA-MIR-153-5P99.8973.866317
HSA-MIR-990299.8969.152250
HSA-MIR-204-5P99.7971.622439
HSA-MIR-211-5P99.7971.652440
HSA-MIR-6505-5P99.7369.251595
HSA-MIR-182599.7268.111089
HSA-MIR-494-3P99.7071.452795
HSA-MIR-320299.6667.702737
HSA-MIR-6832-3P99.5270.441726
HSA-MIR-1212399.5271.792990
HSA-MIR-608199.4866.071446
HSA-MIR-127599.4767.902749
HSA-MIR-391199.3866.951087
HSA-MIR-6853-3P99.3670.791558
HSA-MIR-625-5P99.0268.642031
HSA-MIR-4699-5P98.9967.501210
HSA-MIR-29B-1-5P98.8668.351364
HSA-MIR-4477A98.8369.752952
HSA-MIR-502-5P98.7766.51906
HSA-MIR-4662A-5P98.4867.181007
HSA-MIR-619-3P98.3865.58693
HSA-MIR-18B-3P98.0565.55595
HSA-MIR-63797.9164.051517

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

OrganismSymbolGene ID
danio_rerioC16H1orf43ENSDARG00000055613
ENSDARG00000116978
mus_musculus4933434E20RikENSMUSG00000027942
rattus_norvegicusNs5atp4ENSRNOG00000017758
rattus_norvegicusNs5atp4-ps3ENSRNOG00000027533
drosophila_melanogasterCG6665FBGN0034172

Protein

Protein identifiers

Lipid transport auxiliary protein 1Q9BWL3 (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 IDNamesCanonical?
Q9BWL3-11yes
Q9BWL3-22, Nice-3
Q9BWL3-33
Q9BWL3-44
Q9BWL3-55

RefSeq proteins (8): NP_001092086, NP_001284646, NP_001284647, NP_001284649, NP_001284650, NP_001284652, NP_056264, NP_620077 (=MANE)

Domains & families (InterPro)

IDNameType
IPR010876LTAP1Family

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)

ModelpLDDTFraction very-high
AF-Q9BWL3-F173.350.27

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:

CategoryTerms
cytoplasm3
intracellular membrane-bounded organelle2
cellular anatomical structure2
chordate embryonic development1
endocytosis1
endomembrane system1
organelle membrane contact site1

Protein interactions and networks

STRING

488 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LTAP1EMC7Q9NPA0818
LTAP1CRCT1Q9UGL9657
LTAP1CHMP2AO43633637
LTAP1PSMB4P28070606
LTAP1S100A7AQ86SG5581
LTAP1PSMB2P31145538
LTAP1VPS29Q9UBQ0490
LTAP1OR2T5Q6IEZ7447
LTAP1REEP5Q00765439
LTAP1RAB7AP51149423
LTAP1CNTN3Q9P232415
LTAP1VCPP55072414
LTAP1CFAP141Q5VU69406
LTAP1EMC2Q15006404
LTAP1CABP2Q9NPB3379

IntAct

65 interactions, top by confidence:

ABTypeScore
ENTREP1WWP2psi-mi:“MI:0914”(association)0.850
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
ADCY9NEMP1psi-mi:“MI:0914”(association)0.640
KCNA5TMEM223psi-mi:“MI:0914”(association)0.530
CXCR4TMEM120Bpsi-mi:“MI:0914”(association)0.530
SLC39A4TMEM120Bpsi-mi:“MI:0914”(association)0.530
BTNL3FAM171A2psi-mi:“MI:0914”(association)0.530
KCNS3UPK3BL1psi-mi:“MI:0914”(association)0.530
LRRTM1UPK3BL1psi-mi:“MI:0914”(association)0.530
ZNRF4UPK3BL1psi-mi:“MI:0914”(association)0.530
MRAP2GOLIM4psi-mi:“MI:0914”(association)0.530
GDPD5GOLIM4psi-mi:“MI:0914”(association)0.530
CNGA3C2CD2Lpsi-mi:“MI:0914”(association)0.530
PCDHB7C2CD2Lpsi-mi:“MI:0914”(association)0.530
KCNA10GAPDHSpsi-mi:“MI:0914”(association)0.530
CHRNA9CHEK1psi-mi:“MI:0914”(association)0.530
TEX264PER1psi-mi:“MI:0914”(association)0.530
CHRNDTPST2psi-mi:“MI:0914”(association)0.530
KCNJ6MB21D2psi-mi:“MI:0914”(association)0.530
C1orf43BDKRB1psi-mi:“MI:0915”(physical association)0.370
incESTX7psi-mi:“MI:0914”(association)0.350
KCNA2TMEM129psi-mi:“MI:0914”(association)0.350
TTMPTMEM223psi-mi:“MI:0914”(association)0.350
TTYH1TMEM223psi-mi:“MI:0914”(association)0.350
CHRNA4TMEM223psi-mi:“MI:0914”(association)0.350
OR1M1NBASpsi-mi:“MI:0914”(association)0.350
ZDHHC12NBASpsi-mi:“MI:0914”(association)0.350
IL17RCTMEM131Lpsi-mi:“MI:0914”(association)0.350
PDE3ATMEM131Lpsi-mi:“MI:0914”(association)0.350
SIDT2KLRG2psi-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:

PathwayPartnersFoldFDR
Neurotransmitter receptors and postsynaptic signal transmission712.5×2e-04
Potassium Channels512.0×1e-03
Transmission across Chemical Synapses79.5×4e-04
Neuronal System129.5×8e-07
Transport of small molecules94.0×4e-03

GO biological processes:

GO termPartnersFoldFDR
action potential523.0×5e-04
regulation of membrane potential720.7×2e-05
potassium ion transport614.7×5e-04
monoatomic ion transmembrane transport513.3×2e-03
protein homooligomerization69.4×2e-03
potassium ion transmembrane transport58.7×6e-03
positive regulation of cytosolic calcium ion concentration57.5×1e-02

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance1
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
60011GRCh38/hg38 1q21.3(chr1:153759563-154219803)x1Pathogenic

SpliceAI

941 predictions. Top by Δscore:

VariantEffectΔscore
1:154207647:CC:Cacceptor_gain1.0000
1:154207648:CC:Cacceptor_gain1.0000
1:154212452:GCTTA:Gdonor_loss1.0000
1:154212453:CTTA:Cdonor_loss1.0000
1:154212454:TTACC:Tdonor_loss1.0000
1:154212455:TACC:Tdonor_loss1.0000
1:154212456:ACC:Adonor_gain1.0000
1:154212456:ACCCC:Adonor_loss1.0000
1:154212457:CCC:Cdonor_gain1.0000
1:154212519:ACAC:Adonor_gain1.0000
1:154212520:CACC:Cdonor_gain1.0000
1:154212620:GATCT:Gacceptor_gain1.0000
1:154212621:ATCT:Aacceptor_gain1.0000
1:154212623:CT:Cacceptor_gain1.0000
1:154212624:TCTGT:Tacceptor_loss1.0000
1:154212625:C:CCacceptor_gain1.0000
1:154212626:T:Gacceptor_loss1.0000
1:154214427:A:ACdonor_gain1.0000
1:154214428:C:CCdonor_gain1.0000
1:154214453:ATAC:Adonor_loss1.0000
1:154214454:TACT:Tdonor_loss1.0000
1:154214455:A:ACdonor_gain1.0000
1:154214455:A:ATdonor_loss1.0000
1:154214456:C:CGdonor_loss1.0000
1:154214456:C:CTdonor_gain1.0000
1:154214456:CT:Cdonor_gain1.0000
1:154214465:C:Adonor_gain1.0000
1:154214583:A:Cacceptor_gain1.0000
1:154207644:TAACC:Tacceptor_gain0.9900
1:154207645:AACC:Aacceptor_gain0.9900

AlphaMissense

1649 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:154219905:C:AR33S1.000
1:154219905:C:GR33S1.000
1:154219906:C:AR33M1.000
1:154219906:C:GR33T1.000
1:154220345:G:CS21R1.000
1:154220345:G:TS21R1.000
1:154220347:T:GS21R1.000
1:154220349:C:TG20E1.000
1:154220350:C:GG20R1.000
1:154220350:C:TG20R1.000
1:154207486:C:AK243N0.999
1:154207486:C:GK243N0.999
1:154207499:A:GL239S0.999
1:154212474:G:TA164D0.999
1:154213924:C:AR103S0.999
1:154213924:C:GR103S0.999
1:154213925:C:AR103M0.999
1:154213925:C:GR103T0.999
1:154219843:G:TA54D0.999
1:154219852:C:TG51E0.999
1:154219853:C:GG51R0.999
1:154219853:C:TG51R0.999
1:154219891:A:GF38S0.999
1:154219895:G:TR37S0.999
1:154219900:A:CI35S0.999
1:154219900:A:GI35T0.999
1:154219900:A:TI35N0.999
1:154219903:T:GQ34P0.999
1:154219908:C:AK32N0.999
1:154219908:C:GK32N0.999

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):

StudyTraitp-value
GCST010142_92Fish- and plant-related diet6.000000e-14
GCST010696_22Cortical thickness (min-P)4.000000e-10
GCST010697_50Cortical surface area (min-P)1.000000e-12
GCST010698_81Subcortical volume (min-P)1.000000e-23
GCST010699_7Brain morphology (min-P)1.000000e-10
GCST010700_11Cortical thickness (MOSTest)4.000000e-13
GCST010701_73Cortical surface area (MOSTest)4.000000e-09
GCST010702_45Subcortical volume (MOSTest)4.000000e-10
GCST010703_276Brain morphology (MOSTest)2.000000e-15

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0008111diet measurement
EFO:0004346neuroimaging measurement
EFO:0004840cortical 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.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression, decreases methylation6
aristolochic acid Iincreases expression1
FR900359increases phosphorylation1
triphenyl phosphateaffects expression1
uranyl acetateaffects expression1
bisphenol Aaffects expression1
trichostatin Aaffects expression1
beta-lapachoneincreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
perfluorooctane sulfonic acidincreases expression1
K 7174increases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic aciddecreases expression1
Bortezomibdecreases expression1
Irinotecandecreases expression1
Sunitinibincreases expression1
Cadmiumincreases abundance, increases expression1
Doxorubicinincreases expression1
Gasolineaffects cotreatment, increases abundance, increases expression1
Hydrogen Peroxidedecreases expression, affects cotreatment, increases expression1
Nickelincreases expression1
Polycyclic Aromatic Hydrocarbonsincreases abundance, increases expression, affects cotreatment1
Smokedecreases expression1
Dronabinolincreases expression1
Theophyllineaffects cotreatment, increases expression1
Thiramdecreases expression1
Tobacco Smoke Pollutionincreases expression1
Uraniumaffects expression1
Aflatoxin B1increases expression1

Cellosaurus cell lines

5 cell lines: 4 cancer cell line, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B2T9Abcam HEK293T C1orf43 KOTransformed cell lineFemale
CVCL_SG23HAP1 C1orf43 (-) 1Cancer cell lineMale
CVCL_SG24HAP1 C1orf43 (-) 2Cancer cell lineMale
CVCL_SG25HAP1 C1orf43 (-) 3Cancer cell lineMale
CVCL_SG26HAP1 C1orf43 (-) 4Cancer cell lineMale

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.