GPAT3

Summary

GPAT3 (glycerol-3-phosphate acyltransferase 3, HGNC:28157) is a protein-coding gene on chromosome 4q21.23, encoding Glycerol-3-phosphate acyltransferase 3 (Q53EU6). Converts glycerol-3-phosphate to 1-acyl-sn-glycerol-3-phosphate (lysophosphatidic acid or LPA) by incorporating an acyl moiety at the sn-1 position of the glycerol backbone.

This gene encodes a member of the lysophosphatidic acid acyltransferase protein family. The encoded protein is an enzyme which catalyzes the conversion of glycerol-3-phosphate to lysophosphatidic acid in the synthesis of triacylglycerol. Multiple alternatively spliced variants, encoding the same protein, have been identified.

Source: NCBI Gene 84803 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 75 total
• Druggable target: yes
• MANE Select transcript: NM_032717

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28157
Approved symbol	GPAT3
Name	glycerol-3-phosphate acyltransferase 3
Location	4q21.23
Locus type	gene with protein product
Status	Approved
Aliases	MGC11324, LPAAT-theta, MAG1, HMFN0839, AGPAT10
Ensembl gene	ENSG00000138678
Ensembl biotype	protein_coding
OMIM	610958
Entrez	84803

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 9 protein_coding, 4 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000264409, ENST00000395226, ENST00000506766, ENST00000509044, ENST00000509412, ENST00000513683, ENST00000514309, ENST00000611707, ENST00000860061, ENST00000860062, ENST00000860063, ENST00000860064, ENST00000860065, ENST00000963827

RefSeq mRNA: 3 — MANE Select: NM_032717 NM_001256421, NM_001256422, NM_032717

CCDS: CCDS3606

Canonical transcript exons

ENST00000264409 — 12 exons

Exon	Start	End
ENSE00000935263	83598644	83598723
ENSE00000969788	83598051	83598179
ENSE00001007226	83588210	83588299
ENSE00001007227	83587255	83587329
ENSE00001007228	83594845	83594960
ENSE00001007229	83581562	83581832
ENSE00001007230	83596858	83596913
ENSE00001007232	83597430	83597515
ENSE00001073329	83544536	83544602
ENSE00001073332	83536108	83536763
ENSE00001521003	83604668	83605875
ENSE00003579198	83590199	83590292

Expression profiles

Bgee: expression breadth ubiquitous, 249 present calls, max score 99.62.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.7200 / max 483.3240, expressed in 1404 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
48615	6.0372	1166
48613	2.7317	525
48617	2.1960	568
48614	0.2006	104
48612	0.1981	84
48611	0.1611	65
48621	0.1462	44
48616	0.0490	18

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
kidney epithelium	UBERON:0004819	99.62	gold quality
secondary oocyte	CL:0000655	97.50	gold quality
jejunal mucosa	UBERON:0000399	97.40	gold quality
ileal mucosa	UBERON:0000331	97.10	gold quality
left ventricle myocardium	UBERON:0006566	96.79	gold quality
renal medulla	UBERON:0000362	95.32	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	94.49	gold quality
myocardium	UBERON:0002349	94.29	gold quality
cardiac muscle of right atrium	UBERON:0003379	93.93	gold quality
epithelial cell of pancreas	CL:0000083	93.36	gold quality
esophagus squamous epithelium	UBERON:0006920	92.66	gold quality
buccal mucosa cell	CL:0002336	92.42	gold quality
duodenum	UBERON:0002114	92.20	gold quality
oocyte	CL:0000023	92.01	gold quality
hindlimb stylopod muscle	UBERON:0004252	91.97	gold quality
monocyte	CL:0000576	91.83	gold quality
deltoid	UBERON:0001476	91.71	gold quality
skeletal muscle tissue	UBERON:0001134	91.56	gold quality
leukocyte	CL:0000738	91.55	gold quality
adult organism	UBERON:0007023	91.17	gold quality
quadriceps femoris	UBERON:0001377	90.98	gold quality
vastus lateralis	UBERON:0001379	90.75	gold quality
gastrocnemius	UBERON:0001388	90.55	gold quality
colonic mucosa	UBERON:0000317	90.42	gold quality
adult mammalian kidney	UBERON:0000082	90.31	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	90.29	gold quality
skeletal muscle organ	UBERON:0014892	90.22	gold quality
mucosa of sigmoid colon	UBERON:0004993	90.19	gold quality
muscle tissue	UBERON:0002385	90.13	gold quality
kidney	UBERON:0002113	90.04	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-MTAB-9841	yes	589.50
E-MTAB-6819	yes	164.03
E-CURD-119	yes	36.90
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

77 targeting GPAT3, 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-196A-1-3P	99.99	72.15	2772
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-1229-3P	99.97	66.49	906
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-2110	99.96	66.68	1930
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-6835-3P	99.93	70.49	2904
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-4668-5P	99.79	70.58	3782

Literature-anchored findings (GeneRIF, showing 7)

• LPAAT-theta gene consisted of 12 exons and 11 introns, and mapped to chromosome 4q21.23, was ubiquitously expressed in 18 human tissues and overexpression of LPAAT-theta can induce mTOR-dependent p70S6K and 4EBP1 phosphorylation in HEK293T cells. (PMID:17002884)
• Results reveal a link between the lipogenic effects of insulin and microsomal GPAT3 and GPAT4, implying their importance in glycerolipid biosynthesis. (PMID:20181984)
• findings identified a direct role that mag-1 played in metastasis and implicated its function in cellular adaptation to tumour microenvironment (PMID:22985252)
• Data show that 1-acylglycerol-3-phosphate O-acyltransferase 9 (AGPAT9) inhibit cell growth by regulating expression of KLF4/LASS2/V-ATPase proteins in breast cancer. (PMID:26110566)
• Oligomers of the lipodystrophy protein seipin may co-ordinate GPAT3 and AGPAT2 enzymes to facilitate adipocyte differentiation. (PMID:32094408)
• Mycobacterium leprae promotes triacylglycerol de novo synthesis through induction of GPAT3 expression in human premonocytic THP-1 cells. (PMID:33770127)
• GPAT3 regulates the synthesis of lipid intermediate LPA and exacerbates Kupffer cell inflammation mediated by the ERK signaling pathway. (PMID:36964139)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Gpat3	ENSMUSG00000029314
rattus_norvegicus		ENSRNOG00000085702

Paralogs (4): LPCAT2 (ENSG00000087253), LPCAT1 (ENSG00000153395), GPAT4 (ENSG00000158669), LPCAT4 (ENSG00000176454)

Protein

Protein identifiers

Glycerol-3-phosphate acyltransferase 3 — Q53EU6 (reviewed: Q53EU6)

Alternative names: 1-acyl-sn-glycerol-3-phosphate O-acyltransferase 10, 1-acyl-sn-glycerol-3-phosphate O-acyltransferase 9, Acyl-CoA:glycerol-3-phosphate acyltransferase 3, Lung cancer metastasis-associated protein 1, Lysophosphatidic acid acyltransferase theta, MAG-1

All UniProt accessions (2): Q53EU6, A0A024RDG5

UniProt curated annotations — full annotation on UniProt →

Function. Converts glycerol-3-phosphate to 1-acyl-sn-glycerol-3-phosphate (lysophosphatidic acid or LPA) by incorporating an acyl moiety at the sn-1 position of the glycerol backbone. Also converts 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. Protects cells against lipotoxicity.

Subcellular location. Endoplasmic reticulum membrane.

Tissue specificity. Widely expressed. Expressed in liver, kidney, testis, brain, heart, skeletal muscle, thyroid, prostate, thymus and placenta. Also expressed lung and adipose tissue.

Activity regulation. Inhibited by N-ethylmaleimide (NEM).

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. Glycerolipid metabolism; triacylglycerol biosynthesis. Phospholipid metabolism; CDP-diacylglycerol biosynthesis; CDP-diacylglycerol from sn-glycerol 3-phosphate: step 1/3.

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

RefSeq proteins (3): NP_001243350, NP_001243351, NP_116106* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002123	Plipid/glycerol_acylTrfase	Domain
IPR045252	LPCAT1-like	Domain

Pfam: PF01553

Enzyme classification (BRENDA):

• EC 2.3.1.15 — glycerol-3-phosphate 1-O-acyltransferase (BRENDA: 53 organisms, 165 substrates, 174 inhibitors, 109 Km, 8 kcat entries)

Substrate kinetics (BRENDA)

16 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
SN-GLYCEROL 3-PHOSPHATE	0.021–4.2	29
PALMITOYL-COA	0.002–1.5	20
GLYCEROL 3-PHOSPHATE	0.025–16.4	14
OLEOYL-COA	0.005–0.1	12
STEAROYL-COA	0.004–0.013	4
MYRISTOYL-COA	0.012–0.016	3
PALMITOYL-[ACYL CARRIER PROTEIN]	0.0034–0.015	3
OLEOYL-ACP	0.0028–0.003	2
PALMITOYL-ACP	0.0032–0.0056	2
ACYL-ACP	0.07	1
OLEOYL-[ACYL-CARRIER PROTEIN]	0.0078	1
PALMITOLEOYL-COA	0.0267	1
PALMITOYL-[ACYL-CARRIER PROTEIN]	0.002	1
STEAROYL-ACP	0.0033	1
STEAROYL-[ACYL-CARRIER PROTEIN]	0.0061	1

Catalyzed reactions (Rhea), 12 shown:

• sn-glycerol 3-phosphate + an acyl-CoA = a 1-acyl-sn-glycero-3-phosphate + CoA (RHEA:15325)
• 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)
• sn-glycerol 3-phosphate + hexadecanoyl-CoA = 1-hexadecanoyl-sn-glycero-3-phosphate + CoA (RHEA:35723)
• dodecanoyl-CoA + sn-glycerol 3-phosphate = 1-dodecanoyl-sn-glycerol 3-phosphate + CoA (RHEA:35727)
• 1-(9Z-octadecenoyl)-sn-glycero-3-phosphate + (9Z)-octadecenoyl-CoA = 1,2-di-(9Z-octadecenoyl)-sn-glycero-3-phosphate + CoA (RHEA:37131)
• 1-(9Z,12Z,15Z)-octadecatrienoyl-sn-glycero-3-phosphate + (9Z)-octadecenoyl-CoA = 1-(9Z,12Z,15Z)-octadecatrienoyl-2-(9Z)-octadecenoyl-sn-glycero-3-phosphate + CoA (RHEA:37139)
• 1-(9Z-octadecenoyl)-sn-glycero-3-phosphate + hexadecanoyl-CoA = 1-(9Z)-octadecenoyl-2-hexadecanoyl-sn-glycero-3-phosphate + CoA (RHEA:37143)
• 1-(9Z-octadecenoyl)-sn-glycero-3-phosphate + octadecanoyl-CoA = 1-(9Z-octadecenoyl)-2-octadecanoyl-sn-glycero-3-phosphate + CoA (RHEA:37147)
• 1-(9Z-octadecenoyl)-sn-glycero-3-phosphate + (9Z,12Z)-octadecadienoyl-CoA = 1-(9Z)-octadecenoyl-2-(9Z,12Z)-octadecadienoyl-sn-glycero-3-phosphate + CoA (RHEA:37159)
• 1-(9Z-octadecenoyl)-sn-glycero-3-phosphate + tetradecanoyl-CoA = 1-(9Z)-octadecenoyl-2-tetradecanoyl-sn-glycero-3-phosphate + CoA (RHEA:37171)
• 1-(6Z,9Z,12Z-octadecatrienoyl)-sn-glycero-3-phosphate + (9Z)-octadecenoyl-CoA = (6Z,9Z,12Z)-octadecatrienoyl-2-(9Z)-octadecenoyl-sn-glycero-3-phosphate + CoA (RHEA:37179)

UniProt features (8 total): transmembrane region 3, modified residue 2, chain 1, short sequence motif 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q53EU6-F1	85.50	0.48

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 (2): 68, 77

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-1483166	Synthesis of PA

MSigDB gene sets: 183 (showing top): AP1_01, GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, BENPORATH_ES_WITH_H3K27ME3, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_UP, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, COUP_01, GOBP_PHOSPHOLIPID_BIOSYNTHETIC_PROCESS, BILD_HRAS_ONCOGENIC_SIGNATURE, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, WEI_MYCN_TARGETS_WITH_E_BOX, BACH2_01, GOBP_GLYCEROLIPID_BIOSYNTHETIC_PROCESS, TGANTCA_AP1_C

GO Biological Process (7): glycerol-3-phosphate metabolic process (GO:0006072), phosphatidic acid biosynthetic process (GO:0006654), CDP-diacylglycerol biosynthetic process (GO:0016024), triglyceride biosynthetic process (GO:0019432), regulation of TOR signaling (GO:0032006), lipid metabolic process (GO:0006629), phospholipid biosynthetic process (GO:0008654)

GO Molecular Function (6): 1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841), glycerol-3-phosphate O-acyltransferase activity (GO:0004366), obsolete O-acyltransferase activity (GO:0008374), transferase activity (GO:0016740), acyltransferase activity (GO:0016746), lysophosphatidic acid acyltransferase activity (GO:0042171)

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

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Glycerophospholipid biosynthesis	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
glycerophospholipid biosynthetic process	2
alditol phosphate metabolic process	1
phosphatidic acid metabolic process	1
CDP-diacylglycerol metabolic process	1
triglyceride metabolic process	1
acylglycerol biosynthetic process	1
TOR signaling	1
regulation of intracellular signal transduction	1
primary metabolic process	1
phospholipid metabolic process	1
lipid biosynthetic process	1
organophosphate biosynthetic process	1
acylglycerol O-acyltransferase activity	1
lysophosphatidic acid acyltransferase activity	1
acyltransferase activity, transferring groups other than amino-acyl groups	1
catalytic activity	1
transferase activity	1
lysophospholipid acyltransferase activity	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1620 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GPAT3	GPAM	Q9HCL2	945
GPAT3	GPAT2	Q6NUI2	789
GPAT3	AGPAT2	O15120	750
GPAT3	DGAT2	Q96PD7	728
GPAT3	AGPAT4	Q9NRZ5	709
GPAT3	AGPAT1	Q99943	695
GPAT3	AGPAT3	Q9NRZ7	693
GPAT3	AGPAT5	Q9NUQ2	673
GPAT3	DGAT1	O75907	654
GPAT3	LPIN1	Q14693	636
GPAT3	PPARG	P37231	618
GPAT3	PLIN1	O60240	577
GPAT3	LPIN3	Q9BQK8	541
GPAT3	MOGAT1	Q96PD6	530
GPAT3	EIF4EBP1	Q13541	524

IntAct

60 interactions, top by confidence:

A	B	Type	Score
HRAS	RGL2	psi-mi:“MI:0914”(association)	0.660
NIPAL1	ESYT2	psi-mi:“MI:0914”(association)	0.640
CXCR4	TMEM120B	psi-mi:“MI:0914”(association)	0.530
SLC39A4	TMEM120B	psi-mi:“MI:0914”(association)	0.530
MAS1	POTEF	psi-mi:“MI:0914”(association)	0.530
SLC6A15	CLGN	psi-mi:“MI:0914”(association)	0.530
SLC6A8	ILVBL	psi-mi:“MI:0914”(association)	0.530
SLC6A15	GPR89A	psi-mi:“MI:0914”(association)	0.350
SLC16A11	ESYT2	psi-mi:“MI:0914”(association)	0.350
	FAM171A2	psi-mi:“MI:0914”(association)	0.350
GPAT3	EIF4G3	psi-mi:“MI:0914”(association)	0.350
TSPAN15	TMEM223	psi-mi:“MI:0914”(association)	0.350
CMTM5	TMEM120B	psi-mi:“MI:0914”(association)	0.350
HCST	TMEM120B	psi-mi:“MI:0914”(association)	0.350
ATP2A1	TMEM120B	psi-mi:“MI:0914”(association)	0.350
CACNG1	TMEM120B	psi-mi:“MI:0914”(association)	0.350
TSPAN10	KLRG2	psi-mi:“MI:0914”(association)	0.350
SLC22A4	RTL8C	psi-mi:“MI:0914”(association)	0.350
GPR12	TLCD2	psi-mi:“MI:0914”(association)	0.350
GPR182	SLC12A8	psi-mi:“MI:0914”(association)	0.350
KCNK1	TMEM223	psi-mi:“MI:0914”(association)	0.350
KLRD1	TMEM131L	psi-mi:“MI:0914”(association)	0.350
OPALIN	FAM171A2	psi-mi:“MI:0914”(association)	0.350
MFSD4A	UBXN8	psi-mi:“MI:0914”(association)	0.350
ATP2A3	UBXN8	psi-mi:“MI:0914”(association)	0.350
SPPL2B	HAS3	psi-mi:“MI:0914”(association)	0.350
VIPR1	SLC33A1	psi-mi:“MI:0914”(association)	0.350
SLC2A1	SLC33A1	psi-mi:“MI:0914”(association)	0.350

BioGRID (157): AGPAT9 (Affinity Capture-MS), AGPAT9 (Affinity Capture-MS), AGPAT9 (Affinity Capture-MS), AGPAT9 (Proximity Label-MS), AGPAT9 (Proximity Label-MS), AGPAT9 (Proximity Label-MS), AGPAT9 (Proximity Label-MS), AGPAT9 (Affinity Capture-MS), AGPAT9 (Affinity Capture-RNA), AGPAT9 (Affinity Capture-MS), AGPAT9 (Proximity Label-MS), AGPAT9 (Affinity Capture-MS), AGPAT9 (Proximity Label-MS), AGPAT9 (Proximity Label-MS), AGPAT9 (Proximity Label-MS)

ESM2 similar proteins: A0A0E0S977, A2WV32, A2XN66, A2XNT2, A2Y0X2, A2Z1C8, A2ZAK8, A3FPG8, A3KGT9, C4R4B3, F9WWD1, G2X5A0, G4MWY1, G4YM00, G4Z2L3, G5EBQ8, I1RB03, I1RPI4, O18037, O48946, O48947, O49323, P30628, P78611, Q11087, Q4V8J4, Q53EU6, Q5AMQ4, Q5JN63, Q5R6J7, Q5ZLL8, Q68F37, Q69P51, Q69V23, Q6AT26, Q6DG38, Q84M43, Q84ZN6, Q851L8, Q86UL3

Diamond homologs: A3FPG8, A3KGT9, Q4V8J4, Q53EU6, Q5R6J7, Q5ZLL8, Q68F37, Q6DG38, Q86UL3, Q8C0N2, Q8GWG0, Q8K2C8, Q1HAQ0, Q3TFD2, Q8NF37

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 78 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
R-HSA-425366	5	18.5×	1e-03
SLC-mediated transmembrane transport	7	8.4×	1e-03
Transport of small molecules	10	5.1×	1e-03

GO biological processes:

GO term	Partners	Fold	FDR
adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway	5	15.9×	6e-03
positive regulation of cytosolic calcium ion concentration	6	10.2×	6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	62
Likely benign	0
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1953 predictions. Top by Δscore:

Variant	Effect	Δscore
4:83536011:GGGC:G	donor_gain	1.0000
4:83536012:GGC:G	donor_gain	1.0000
4:83536014:C:CG	donor_gain	1.0000
4:83536502:A:AG	acceptor_gain	1.0000
4:83536502:AGAG:A	acceptor_gain	1.0000
4:83536503:G:GG	acceptor_gain	1.0000
4:83536503:GAGG:G	acceptor_gain	1.0000
4:83536760:AGAGG:A	donor_loss	1.0000
4:83536761:GAG:G	donor_gain	1.0000
4:83536762:AGGTG:A	donor_loss	1.0000
4:83536764:G:GA	donor_loss	1.0000
4:83536764:G:GG	donor_gain	1.0000
4:83536765:T:A	donor_loss	1.0000
4:83536766:GAGT:G	donor_loss	1.0000
4:83544530:GAACA:G	acceptor_loss	1.0000
4:83544531:AACAG:A	acceptor_loss	1.0000
4:83544532:ACAG:A	acceptor_loss	1.0000
4:83544532:ACAGT:A	acceptor_gain	1.0000
4:83544533:CA:C	acceptor_loss	1.0000
4:83544534:A:AC	acceptor_loss	1.0000
4:83544534:A:AG	acceptor_gain	1.0000
4:83544534:AGT:A	acceptor_gain	1.0000
4:83544534:AGTG:A	acceptor_gain	1.0000
4:83544534:AGTGG:A	acceptor_gain	1.0000
4:83544535:G:C	acceptor_loss	1.0000
4:83544535:G:GA	acceptor_gain	1.0000
4:83544535:GT:G	acceptor_gain	1.0000
4:83544535:GTG:G	acceptor_gain	1.0000
4:83544535:GTGG:G	acceptor_gain	1.0000
4:83544535:GTGGG:G	acceptor_gain	1.0000

AlphaMissense

2833 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:83590239:C:G	H229D	1.000
4:83590241:T:A	H229Q	1.000
4:83590241:T:G	H229Q	1.000
4:83597437:C:G	C306W	1.000
4:83597446:T:A	N309K	1.000
4:83597446:T:G	N309K	1.000
4:83598078:T:A	W342R	1.000
4:83598078:T:C	W342R	1.000
4:83598132:T:A	W360R	1.000
4:83598132:T:C	W360R	1.000
4:83581699:T:C	F116L	0.999
4:83581701:T:A	F116L	0.999
4:83581701:T:G	F116L	0.999
4:83581723:T:A	W124R	0.999
4:83581723:T:C	W124R	0.999
4:83581795:G:C	G148R	0.999
4:83581832:G:T	R160M	0.999
4:83590231:T:A	V226D	0.999
4:83590234:C:A	A227D	0.999
4:83590238:C:A	N228K	0.999
4:83590238:C:G	N228K	0.999
4:83590239:C:A	H229N	0.999
4:83590254:G:C	D234H	0.999
4:83590255:A:T	D234V	0.999
4:83594917:T:C	F271L	0.999
4:83594919:T:A	F271L	0.999
4:83594919:T:G	F271L	0.999
4:83596899:T:C	L299P	0.999
4:83596904:T:C	F301L	0.999
4:83596906:T:A	F301L	0.999

dbSNP variants (sampled 300 via entrez): RS1000010067 (4:83564906 G>A), RS1000017864 (4:83602431 C>G), RS1000111549 (4:83558229 A>C,T), RS1000141534 (4:83540684 T>C), RS1000142175 (4:83548282 T>G), RS1000154265 (4:83571438 C>T), RS10002139 (4:83568493 C>T), RS1000219173 (4:83558685 C>G,T), RS1000228132 (4:83557905 A>G), RS1000228285 (4:83605708 A>G,T), RS1000252964 (4:83565466 G>A,T), RS1000338723 (4:83598128 C>A,T), RS1000449133 (4:83605140 G>A), RS1000528605 (4:83538694 A>T), RS1000551460 (4:83603310 G>T)

Disease associations

OMIM: gene MIM:610958 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST001762_177	Obesity-related traits	9.000000e-06
GCST006979_437	Heel bone mineral density	6.000000e-13

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004627	IGF-1 measurement
EFO:0009270	heel bone mineral density

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4523318 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases mutagenesis, increases expression	7
Cyclosporine	increases expression	7
Tetrachlorodibenzodioxin	increases expression, decreases reaction	5
sodium arsenite	increases expression	4
Air Pollutants	increases abundance, increases expression, decreases expression	3
Cisplatin	affects cotreatment, decreases expression, increases expression	3
Smoke	decreases expression, increases expression	3
Tobacco Smoke Pollution	increases expression	3
Valproic Acid	affects expression, increases expression	3
sulforaphane	increases expression	2
mercuric bromide	increases expression, affects cotreatment	2
Ampicillin	decreases expression	2
Nickel	decreases expression, increases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Quercetin	increases expression	2
Tretinoin	increases expression	2
Aflatoxin B1	decreases methylation, increases expression	2
Cadmium Chloride	increases expression	2
p-Chloromercuribenzoic Acid	increases expression, affects cotreatment	2
Particulate Matter	increases expression, decreases expression, increases abundance	2
chloroacetaldehyde	increases expression	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
lead acetate	increases expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
1,2-diamino-4-nitrobenzene	increases expression	1
ethyl-p-hydroxybenzoate	increases expression	1
beta-lapachone	increases expression	1
arsenite	affects expression	1

ChEMBL screening assays

6 unique, capped per target: 6 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL4482378	Binding	Inhibition of GPAT3 (unknown origin) expressed in Sf9 cell membranes assessed as reduction in glycerol 3-phosphate acyltransferase activity at 10 uM using [3H]-glycerol 3-phosphate and palmitoyl CoA incubated for 60 mins by scintillation co	Test system for measuring mest activity as well as methods and uses involving the same

Clinical trials (associated diseases)

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