◎ Sugi Atlas

Atlas / Gene / LCLAT1

LCLAT1

gene
On this page

Also known as FLJ37965ALCAT1AGPAT8LPLAT6

Summary

LCLAT1 (lysocardiolipin acyltransferase 1, HGNC:26756) is a protein-coding gene on chromosome 2p23.1, encoding Lysocardiolipin acyltransferase 1 (Q6UWP7). Exhibits acyl-CoA:lysocardiolipin acyltransferase (ALCAT) activity; catalyzes the reacylation of lyso-cardiolipin to cardiolipin (CL), a key step in CL remodeling.

Enables 1-acylglycerol-3-phosphate O-acyltransferase activity. Predicted to be involved in phosphatidylinositol acyl-chain remodeling. Located in cytosol and endoplasmic reticulum.

Source: NCBI Gene 253558 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 75 total
  • Druggable target: yes
  • MANE Select transcript: NM_001002257

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26756
Approved symbolLCLAT1
Namelysocardiolipin acyltransferase 1
Location2p23.1
Locus typegene with protein product
StatusApproved
AliasesFLJ37965, ALCAT1, AGPAT8, LPLAT6
Ensembl geneENSG00000172954
Ensembl biotypeprotein_coding
OMIM614241
Entrez253558

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 22 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000309052, ENST00000319406, ENST00000379509, ENST00000465200, ENST00000465538, ENST00000466477, ENST00000476038, ENST00000476535, ENST00000478015, ENST00000488144, ENST00000491680, ENST00000497423, ENST00000897444, ENST00000897445, ENST00000897446, ENST00000897447, ENST00000897448, ENST00000897449, ENST00000897450, ENST00000897451, ENST00000897452, ENST00000921891, ENST00000921892, ENST00000921893

RefSeq mRNA: 4 — MANE Select: NM_001002257 NM_001002257, NM_001304445, NM_001304446, NM_182551

CCDS: CCDS1772, CCDS42670

Canonical transcript exons

ENST00000379509 — 6 exons

ExonStartEnd
ENSE000015213133044724630447383
ENSE000019475933064011730644225
ENSE000034842653056214630562292
ENSE000035033443052558730525755
ENSE000035386583056806030568176
ENSE000036317753053311630533314

Expression profiles

Bgee: expression breadth ubiquitous, 256 present calls, max score 98.07.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.3133 / max 3101.1273, expressed in 1790 samples.

FANTOM5 promoters (21 alternative TSS)

Promoter IDTPM avgSamples expressed
195849.15171703
195859.05081651
196032.31611004
196100.261097
195870.256897
195860.237587
195990.188956
196050.162844
196110.150441
196080.099326

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
left ventricle myocardiumUBERON:000656698.07gold quality
epithelial cell of pancreasCL:000008396.03gold quality
ileal mucosaUBERON:000033195.20gold quality
myocardiumUBERON:000234994.03gold quality
pancreatic ductal cellCL:000207993.92gold quality
kidney epitheliumUBERON:000481993.47gold quality
endothelial cellCL:000011593.12silver quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047392.75gold quality
jejunal mucosaUBERON:000039992.46gold quality
saphenous veinUBERON:000731892.21gold quality
heart right ventricleUBERON:000208092.16gold quality
bronchial epithelial cellCL:000232891.14gold quality
urethraUBERON:000005791.13gold quality
bronchusUBERON:000218590.74gold quality
cardiac muscle of right atriumUBERON:000337990.68gold quality
epithelium of nasopharynxUBERON:000195190.38gold quality
nasopharynxUBERON:000172890.37gold quality
jejunumUBERON:000211590.34gold quality
tibialis anteriorUBERON:000138590.21gold quality
visceral pleuraUBERON:000240189.38gold quality
corpus epididymisUBERON:000435989.03gold quality
deltoidUBERON:000147688.95gold quality
duodenumUBERON:000211488.69gold quality
upper arm skinUBERON:000426388.55gold quality
palpebral conjunctivaUBERON:000181288.48gold quality
caput epididymisUBERON:000435888.33gold quality
calcaneal tendonUBERON:000370188.12gold quality
esophagus squamous epitheliumUBERON:000692087.91gold quality
oviduct epitheliumUBERON:000480487.80gold quality
tibiaUBERON:000097987.79gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes6.13

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

211 targeting LCLAT1, 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-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-4262100.0073.263931
HSA-MIR-188-3P100.0068.761240
HSA-MIR-4682100.0068.891258
HSA-MIR-340-5P100.0072.504437
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-3646100.0073.565283
HSA-MIR-574-5P100.0066.01989
HSA-MIR-366299.9973.825684
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-428299.9975.366408
HSA-MIR-548AW99.9972.573559
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-186-5P99.9970.833707
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-548P99.9872.253784
HSA-MIR-477599.9875.006394
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-56899.9869.862084
HSA-MIR-1213699.9872.815713

Literature-anchored findings (GeneRIF, showing 6)

  • Data show that ALCAT1 possesses acyltransferase activities toward lysophosphatidylinositol and lysophosphatidylglycerol, and identify critical amino acids that are potentially involved in lysophospholipid substrate binding. (PMID:19075029)
  • LYCAT expression was significantly altered in PBMCs and lung tissues from patients with idiopathic pulmonary fibrosis. (PMID:24779708)
  • LYCAT regulates TGF-beta mediated lung fibroblast differentiation in pulmonary fibrosis. (PMID:28751023)
  • Lysocardiolipin acyltransferase regulates NSCLC cell proliferation and migration by modulating mitochondrial dynamics. (PMID:32732285)
  • Long non-coding RNA DNMBP-AS1 promotes prostate cancer development by regulating LCLAT1. (PMID:36602957)
  • ALCAT1-mediated abnormal cardiolipin remodelling promotes mitochondrial injury in podocytes in diabetic kidney disease. (PMID:38200543)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_reriolclat1ENSDARG00000103320
mus_musculusLclat1ENSMUSG00000054469
rattus_norvegicusLclat1ENSRNOG00000034026
caenorhabditis_elegansWBGENE00020264
caenorhabditis_elegansWBGENE00022646
caenorhabditis_elegansWBGENE00044631

Paralogs (4): AGPAT4 (ENSG00000026652), LPGAT1 (ENSG00000123684), AGPAT5 (ENSG00000155189), AGPAT3 (ENSG00000160216)

Protein

Protein identifiers

Lysocardiolipin acyltransferase 1 — Q6UWP7 (reviewed: Q6UWP7)

Alternative names: 1-acylglycerol-3-phosphate O-acyltransferase 8, Acyl-CoA:lysocardiolipin acyltransferase 1

All UniProt accessions (9): Q6UWP7, C9J5S5, C9J6F4, C9JA02, C9JMW2, C9JUV9, C9JXY8, C9K0C3, F8WEY2

UniProt curated annotations — full annotation on UniProt →

Function. Exhibits acyl-CoA:lysocardiolipin acyltransferase (ALCAT) activity; catalyzes the reacylation of lyso-cardiolipin to cardiolipin (CL), a key step in CL remodeling. Recognizes both monolysocardiolipin and dilysocardiolipin as substrates with a preference for linoleoyl-CoA and oleoyl-CoA as acyl donors. Also exhibits 1-acyl-sn-glycerol-3-phosphate acyltransferase activity (AGPAT) activity; converts 1-acyl-sn-glycerol-3- phosphate (lysophosphatidic acid or LPA) into 1,2-diacyl-sn-glycerol-3- phosphate (phosphatidic acid or PA) by incorporating an acyl moiety at the sn-2 position of the glycerol backbone. Possesses both lysophosphatidylinositol acyltransferase (LPIAT) and lysophosphatidylglycerol acyltransferase (LPGAT) activities. Required for establishment of the hematopoietic and endothelial lineages.

Subcellular location. Endoplasmic reticulum membrane.

Tissue specificity. Expressed at higher level in heart, kidney and pancreas than in brain, spleen, liver, lung, small intestine and placenta.

Domain organisation. The HXXXXD motif is essential for acyltransferase activity and may constitute the binding site for the phosphate moiety of the glycerol-3-phosphate.

Pathway. Phospholipid metabolism; CDP-diacylglycerol biosynthesis; CDP-diacylglycerol from sn-glycerol 3-phosphate: step 2/3.

Similarity. Belongs to the 1-acyl-sn-glycerol-3-phosphate acyltransferase family.

Isoforms (3)

UniProt IDNamesCanonical?
Q6UWP7-11yes
Q6UWP7-22
Q6UWP7-33

RefSeq proteins (4): NP_001002257, NP_001291374, NP_001291375, NP_872357 (=MANE)

Domains & families (InterPro)

IDNameType
IPR002123Plipid/glycerol_acylTrfaseDomain
IPR032098Acyltransf_CDomain

Pfam: PF01553, PF16076

Catalyzed reactions (Rhea), 12 shown:

  • a 1-acyl-sn-glycero-3-phosphate + an acyl-CoA = a 1,2-diacyl-sn-glycero-3-phosphate + CoA (RHEA:19709)
  • 1-hexadecanoyl-sn-glycero-3-phosphate + (9Z)-octadecenoyl-CoA = 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphate + CoA (RHEA:33187)
  • a 1-acyl-sn-glycero-3-phospho-(1D-myo-inositol) + an acyl-CoA = a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol) + CoA (RHEA:33195)
  • 1-acyl-sn-glycero-3-phospho-(1’-sn-glycerol) + an acyl-CoA = a 1,2-diacyl-sn-glycero-3-phospho-(1’-sn-glycerol) + CoA (RHEA:33203)
  • 1-hexadecanoyl-sn-glycero-3-phospho-(1’-sn-glycerol) + hexadecanoyl-CoA = 1,2-dihexadecanoyl-sn-glycero-3-phospho-(1’-sn-glycerol) + CoA (RHEA:35851)
  • 1-hexadecanoyl-sn-glycero-3-phospho-(1D-myo-inositol) + (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA = 1-hexadecanoyl-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phospho-D-myo-inositol + CoA (RHEA:35867)
  • 1-hexadecanoyl-sn-glycero-3-phospho-(1D-myo-inositol) + hexadecanoyl-CoA = 1,2-dihexadecanoyl-sn-glycero-3-phospho-(1D-myo-inositol) + CoA (RHEA:35871)
  • 1-hexadecanoyl-sn-glycero-3-phospho-(1D-myo-inositol) + octadecanoyl-CoA = 1-hexadecanoyl-2-octadecanoyl-sn-glycero-3-phospho-(1D-myo-inositol) + CoA (RHEA:35875)
  • 1-hexadecanoyl-sn-glycero-3-phospho-(1D-myo-inositol) + (9Z)-octadecenoyl-CoA = 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phospho-(1D-myo-inositol) + CoA (RHEA:35879)
  • 1-hexadecanoyl-sn-glycero-3-phospho-(1D-myo-inositol) + (9Z,12Z)-octadecadienoyl-CoA = 1-hexadecanoyl-2-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phospho-(1D-myo-inositol) + CoA (RHEA:35883)
  • 1-hexadecanoyl-sn-glycero-3-phospho-(1’-sn-glycerol) + octadecanoyl-CoA = 1-hexadecanoyl-2-octadecanoyl-sn-glycero-3-phospho-(1’-sn-glycerol) + CoA (RHEA:35887)
  • 1-hexadecanoyl-sn-glycero-3-phospho-(1’-sn-glycerol) + (9Z)-octadecenoyl-CoA = 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phospho-(1’-sn-glycerol) + CoA (RHEA:35891)

UniProt features (14 total): transmembrane region 4, mutagenesis site 3, splice variant 3, chain 1, sequence variant 1, short sequence motif 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6UWP7-F189.620.85

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 (1): 221

Mutagenesis-validated functional residues (3):

PositionPhenotype
206abolishes lpiat and lpgat activities.
206does not increase enzyme activity.
207abolishes lpiat activity. no effect on lpgat activity.

Function

Pathways and Gene Ontology

Reactome pathways

6 pathways

IDPathway
R-HSA-1482798Acyl chain remodeling of CL
R-HSA-1483166Synthesis of PA
R-HSA-1430728Metabolism
R-HSA-1483206Glycerophospholipid biosynthesis
R-HSA-1483257Phospholipid metabolism
R-HSA-556833Metabolism of lipids

MSigDB gene sets: 231 (showing top): GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLINOSITOL_METABOLIC_PROCESS, TGCACTT_MIR519C_MIR519B_MIR519A, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GTTAAAG_MIR302B, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLGLYCEROL_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_PHOSPHOLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, GTGCCTT_MIR506, GOBP_GLYCEROLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROPHOSPHOLIPID_METABOLIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS, GOBP_LIPID_BIOSYNTHETIC_PROCESS

GO Biological Process (6): phosphatidic acid biosynthetic process (GO:0006654), CDP-diacylglycerol biosynthetic process (GO:0016024), cardiolipin acyl-chain remodeling (GO:0035965), phosphatidylinositol acyl-chain remodeling (GO:0036149), lipid metabolic process (GO:0006629), phospholipid biosynthetic process (GO:0008654)

GO Molecular Function (5): 1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841), obsolete O-acyltransferase activity (GO:0008374), acyltransferase activity (GO:0016746), protein binding (GO:0005515), transferase activity (GO:0016740)

GO Cellular Component (5): endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), cytosol (GO:0005829), endomembrane system (GO:0012505), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
Glycerophospholipid biosynthesis2
Phospholipid metabolism1
Metabolism of lipids1
Metabolism1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
glycerophospholipid biosynthetic process2
cytoplasm2
phosphatidic acid metabolic process1
CDP-diacylglycerol metabolic process1
cardiolipin metabolic process1
phosphatidylinositol metabolic process1
primary metabolic process1
phospholipid metabolic process1
lipid biosynthetic process1
organophosphate biosynthetic process1
acylglycerol O-acyltransferase activity1
lysophosphatidic acid acyltransferase activity1
transferase activity1
binding1
catalytic activity1
endomembrane system1
intracellular membrane-bounded organelle1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
vacuole1
plasma membrane1

Protein interactions and networks

STRING

1676 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LCLAT1TAFAZZINQ16635758
LCLAT1LPCAT4Q643R3660
LCLAT1CRLS1Q9UJA2649
LCLAT1TAMM41Q96BW9527
LCLAT1AGPAT1Q99943505
LCLAT1GPAT4Q86UL3486
LCLAT1SPTSSBQ8NFR3472
LCLAT1AGPAT2O15120457
LCLAT1LPCAT1Q8NF37454
LCLAT1PNPLA8Q9NP80452
LCLAT1PGS1Q32NB8452
LCLAT1YPEL5P62699447
LCLAT1LPCAT2Q7L5N7438
LCLAT1GPAT3Q53EU6433
LCLAT1CDIPTO14735431

IntAct

89 interactions, top by confidence:

ABTypeScore
NIPAL1ESYT2psi-mi:“MI:0914”(association)0.640
FAM174AGAKpsi-mi:“MI:0914”(association)0.640
TRDNTMEM223psi-mi:“MI:0914”(association)0.640
LCLAT1LNX1psi-mi:“MI:0915”(physical association)0.560
GOPCLCLAT1psi-mi:“MI:0915”(physical association)0.560
LNX1LCLAT1psi-mi:“MI:0915”(physical association)0.560
LCLAT1GOPCpsi-mi:“MI:0915”(physical association)0.560
LCLAT1PICK1psi-mi:“MI:0915”(physical association)0.560
ADGRG5KLRG2psi-mi:“MI:0914”(association)0.530
SLC30A2RER1psi-mi:“MI:0914”(association)0.530
PRRT2NDUFS4psi-mi:“MI:0914”(association)0.530
ADAM21PLXNA2psi-mi:“MI:0914”(association)0.530
TSPAN5SC5Dpsi-mi:“MI:0914”(association)0.530
FAM174ABLTP3Bpsi-mi:“MI:0914”(association)0.530
CD63LGALS8psi-mi:“MI:0914”(association)0.530
SIDT2AP3D1psi-mi:“MI:0914”(association)0.530
ANKRD22ESYT2psi-mi:“MI:0914”(association)0.530
ATP1A3AGPAT2psi-mi:“MI:0914”(association)0.530
KCNA2FADS1psi-mi:“MI:0914”(association)0.530
LPAR1TMEM223psi-mi:“MI:0914”(association)0.530
UNC93B1psi-mi:“MI:0914”(association)0.350
TMEM223psi-mi:“MI:0914”(association)0.350
PAESYT2psi-mi:“MI:0914”(association)0.350
COPAESYT2psi-mi:“MI:0914”(association)0.350
COPB2ESYT2psi-mi:“MI:0914”(association)0.350

BioGRID (121): LCLAT1 (Two-hybrid), LCLAT1 (Two-hybrid), LCLAT1 (Affinity Capture-MS), LCLAT1 (Affinity Capture-MS), LCLAT1 (Affinity Capture-MS), LCLAT1 (Affinity Capture-MS), LCLAT1 (Affinity Capture-MS), LCLAT1 (Affinity Capture-MS), LCLAT1 (Affinity Capture-MS), LCLAT1 (Affinity Capture-MS), LCLAT1 (Proximity Label-MS), LCLAT1 (Affinity Capture-MS), LCLAT1 (Affinity Capture-MS), LCLAT1 (Affinity Capture-MS), LCLAT1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1V6NVX3, A2BGU9, F1QCP6, G5EDL5, H2E7T6, O02218, O14169, O94361, P17625, P34426, P41879, P54840, Q06510, Q08650, Q0KHU5, Q11087, Q16635, Q20800, Q22267, Q24093, Q28C60, Q3UN02, Q41745, Q4V8A1, Q54DX7, Q5F3X0, Q6DCK1, Q6IV76, Q6IV77, Q6IV78, Q6IV82, Q6IV83, Q6IV84, Q6IWY1, Q6UWP7, Q75BY0, Q8LG50, Q8VCB3, Q91WF0, Q91YX5

Diamond homologs: Q11087, Q20800, Q3UN02, Q5F3X0, Q6NYV8, Q6UWP7, Q8L4Y2, Q91YX5, Q92604, Q9LHN4, Q41745, Q5RA57, Q9NRZ7, P33333, Q4R581, Q5E9R2, Q5R757, Q6IWY1, Q8K4X7, Q8LG50, Q924S1, Q9D1E8, Q9D517, Q9NRZ5, Q9NUQ2, Q9SYC8, Q9XFW4, O94361, Q9US20, Q12185

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 118 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.

GO biological processes:

GO termPartnersFoldFDR
retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum516.4×5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance49
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3065 predictions. Top by Δscore:

VariantEffectΔscore
2:30533111:CTTA:Cacceptor_loss1.0000
2:30533112:TTAG:Tacceptor_loss1.0000
2:30533113:TAGGC:Tacceptor_loss1.0000
2:30533114:A:AGacceptor_gain1.0000
2:30533114:AG:Aacceptor_gain1.0000
2:30533114:AGGC:Aacceptor_loss1.0000
2:30533115:G:GGacceptor_gain1.0000
2:30533115:GG:Gacceptor_gain1.0000
2:30533115:GGC:Gacceptor_gain1.0000
2:30533115:GGCA:Gacceptor_gain1.0000
2:30533312:TTGG:Tdonor_loss1.0000
2:30533314:GGTA:Gdonor_loss1.0000
2:30533315:G:GAdonor_loss1.0000
2:30533315:G:GGdonor_gain1.0000
2:30533316:T:Gdonor_loss1.0000
2:30568054:GTTTA:Gacceptor_loss1.0000
2:30568055:TTTA:Tacceptor_loss1.0000
2:30568056:TTA:Tacceptor_loss1.0000
2:30568058:A:AGacceptor_gain1.0000
2:30568059:G:GAacceptor_loss1.0000
2:30568059:G:GGacceptor_gain1.0000
2:30568173:GAAG:Gdonor_gain1.0000
2:30568174:AAGGT:Adonor_loss1.0000
2:30568175:AGGT:Adonor_loss1.0000
2:30568177:G:GGdonor_gain1.0000
2:30568177:GTA:Gdonor_loss1.0000
2:30568178:T:Adonor_loss1.0000
2:30447306:G:GTdonor_gain0.9900
2:30525586:GAATC:Gacceptor_gain0.9900
2:30525752:TGTGG:Tdonor_loss0.9900

AlphaMissense

2507 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:30533202:C:AN122K1.000
2:30533202:C:GN122K1.000
2:30533203:C:GH123D1.000
2:30533221:T:AW129R1.000
2:30533221:T:CW129R1.000
2:30533189:T:AV118D0.999
2:30533205:T:AH123Q0.999
2:30533205:T:GH123Q0.999
2:30533218:G:CD128H0.999
2:30533219:A:CD128A0.999
2:30533219:A:TD128V0.999
2:30533233:T:AW133R0.999
2:30533233:T:CW133R0.999
2:30533285:A:TK150I0.999
2:30533286:A:CK150N0.999
2:30533286:A:TK150N0.999
2:30562175:T:CF170L0.999
2:30562177:C:AF170L0.999
2:30562177:C:GF170L0.999
2:30562185:G:CR173T0.999
2:30562185:G:TR173M0.999
2:30562268:T:CF201L0.999
2:30562270:C:AF201L0.999
2:30562270:C:GF201L0.999
2:30562277:G:AG204R0.999
2:30562277:G:CG204R0.999
2:30562277:G:TG204W0.999
2:30640296:T:AW308R0.999
2:30640296:T:CW308R0.999
2:30640298:G:CW308C0.999

dbSNP variants (sampled 300 via entrez): RS1000023324 (2:30603438 G>T), RS1000032117 (2:30594355 C>T), RS1000057780 (2:30563361 A>G), RS1000083893 (2:30594227 C>G), RS1000108570 (2:30486589 C>T), RS1000120140 (2:30636435 G>A), RS1000134226 (2:30580025 C>G,T), RS1000135682 (2:30562468 T>C), RS1000151952 (2:30529798 G>A), RS1000174176 (2:30540911 C>A,T), RS1000185197 (2:30570260 T>C), RS1000214086 (2:30453955 G>T), RS1000243098 (2:30563938 CTTTTTT>C,CTTTTT,CTTTTTTT), RS1000251931 (2:30461927 C>A,T), RS1000253508 (2:30513866 C>T)

Disease associations

OMIM: gene MIM:614241 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST004286_1Midgestational circulating levels of PBDEs (fetal genetic effect)2.000000e-07
GCST90011900_179Serum alkaline phosphatase levels1.000000e-14
GCST90013406_193Liver enzyme levels (alkaline phosphatase)2.000000e-18

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0007959fetal genotype effect measurement
EFO:0007961polybrominated biphenyl measurement
EFO:0007962polybrominated diphenyl ether measurement
EFO:0007964gestational serum measurement
EFO:0004533alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5169167 (SINGLE PROTEIN)

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

ChEMBL bioactivities

109 potent at pChembl≥5 of 109 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
8.10IC508nMCHEMBL5824878
7.75IC5018nMCHEMBL5767889
7.72IC5019nMCHEMBL5831650
7.72IC5019nMCHEMBL6012165
7.72IC5019nMCHEMBL5961231
7.72IC5019nMCHEMBL5949570
7.72IC5019nMCHEMBL5883583
7.70IC5020nMCHEMBL6022208
7.68IC5021nMCHEMBL5906008
7.68IC5021nMCHEMBL5945773
7.62IC5024nMCHEMBL5873285
7.62IC5024nMCHEMBL5929888
7.62IC5024nMCHEMBL5930269
7.60IC5025nMCHEMBL5952262
7.58IC5026nMCHEMBL5975376
7.58IC5026nMCHEMBL6033967
7.55IC5028nMCHEMBL5790548
7.54IC5029nMCHEMBL5784269
7.54IC5029nMCHEMBL5889305
7.52IC5030nMCHEMBL5769263
7.51IC5031nMCHEMBL5993249
7.51IC5031nMCHEMBL6005398
7.48IC5033nMCHEMBL6023196
7.48IC5033nMCHEMBL5959587
7.47IC5034nMCHEMBL5745104
7.47IC5034nMCHEMBL5977313
7.44IC5036nMCHEMBL5925852
7.42IC5038nMCHEMBL1598822
7.42IC5038nMCHEMBL5883872
7.42IC5038nMCHEMBL6010869
7.41IC5039nMCHEMBL5911486
7.34IC5046nMCHEMBL5964853
7.33IC5047nMCHEMBL5822238
7.32IC5048nMCHEMBL5939492
7.22IC5060nMCHEMBL5845311
7.22IC5060nMCHEMBL5765477
7.21IC5062nMCHEMBL5741133
7.21IC5061nMCHEMBL6032700
7.21IC5062nMCHEMBL5852440
7.19IC5064nMCHEMBL5977341
7.18IC5066nMCHEMBL5989881
7.17IC5067nMCHEMBL5910432
7.17IC5067nMCHEMBL5914446
7.17IC5067nMCHEMBL6063174
7.14IC5072nMCHEMBL5749955
7.14IC5072nMCHEMBL5968191
7.12IC5076nMCHEMBL5909449
7.11IC5078nMCHEMBL6007709
7.10IC5079nMCHEMBL5864133
7.06IC5087nMCHEMBL6056576

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyrenedecreases expression, increases methylation2
Particulate Matterdecreases expression, increases abundance, increases expression2
aristolochic acid Idecreases expression1
triphenyl phosphateaffects expression1
trichostatin Aaffects expression1
sodium arsenitedecreases expression1
CGP 52608affects binding, increases reaction1
ICG 001decreases expression1
abrinedecreases expression1
jinfukangaffects cotreatment, decreases expression1
Acetaminophendecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Cisplatinaffects cotreatment, decreases expression1
Diurondecreases expression1
Gallic Aciddecreases expression1
Ivermectindecreases expression1
Dronabinolincreases expression1
Thiramdecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Tretinoindecreases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression1
Cyclosporinedecreases expression1
Aflatoxin B1decreases expression1

ChEMBL screening assays

3 unique, capped per target: 3 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5116771BindingSubstrate activity at recombinant human ALCAT1 expressed in HEK293 cells using oleoyl-CoA as substrate assessed as acylated product formation by Rapidfire-triple quad mass spectrometry analysisSynthesis of biotinylated-LPG as a chemical biology tool enabling discovery of ALCAT1 modulators. — Bioorg Med Chem Lett

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 78

This page pulls from 78 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_assaychembl_documentchembl_moleculechembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomereactomeparentrefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot