GPAT2

Summary

GPAT2 (glycerol-3-phosphate acyltransferase 2, mitochondrial, HGNC:27168) is a protein-coding gene on chromosome 2q11.2, encoding Glycerol-3-phosphate acyltransferase 2, mitochondrial (Q6NUI2). Transfers an acyl-group from acyl-ACP to the sn-1 position of glycerol-3-phosphate producing a lysophosphatidic acid (LPA), an essential step for the triacylglycerol (TAG) and glycerophospholipids. It is a selective cancer dependency (DepMap: 32.1% of cell lines).

Enables glycerol-3-phosphate O-acyltransferase activity. Predicted to be involved in glycerol-3-phosphate metabolic process; glycerolipid biosynthetic process; and piRNA processing. Located in mitochondrion.

Source: NCBI Gene 150763 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 130 total — 3 likely-pathogenic
• Cancer dependency (DepMap): dependent in 32.1% of screened cell lines
• MANE Select transcript: NM_001321527

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27168
Approved symbol	GPAT2
Name	glycerol-3-phosphate acyltransferase 2, mitochondrial
Location	2q11.2
Locus type	gene with protein product
Status	Approved
Aliases	CT123
Ensembl gene	ENSG00000186281
Ensembl biotype	protein_coding
OMIM	616431
Entrez	150763

Gene structure

Transcript identifiers

Ensembl transcripts: 39 — 33 protein_coding, 4 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000359548, ENST00000434632, ENST00000439254, ENST00000453542, ENST00000468438, ENST00000471757, ENST00000482704, ENST00000484440, ENST00000486463, ENST00000488515, ENST00000687910, ENST00000691940, ENST00000862208, ENST00000862209, ENST00000862210, ENST00000862211, ENST00000862212, ENST00000862213, ENST00000862214, ENST00000862215, ENST00000862216, ENST00000862217, ENST00000862218, ENST00000964151, ENST00000964152, ENST00000964153, ENST00000964154, ENST00000964155, ENST00000964156, ENST00000964157, ENST00000964158, ENST00000964159, ENST00000964160, ENST00000964161, ENST00000964162, ENST00000964163, ENST00000964164, ENST00000964165, ENST00000964166

RefSeq mRNA: 9 — MANE Select: NM_001321527 NM_001321525, NM_001321526, NM_001321527, NM_001321528, NM_001321529, NM_001321530, NM_001321531, NM_001389639, NM_207328

CCDS: CCDS42714, CCDS82482, CCDS92810, CCDS92811

Canonical transcript exons

ENST00000434632 — 22 exons

Exon	Start	End
ENSE00001791718	96034853	96034916
ENSE00003460912	96026183	96026305
ENSE00003465984	96027007	96027106
ENSE00003466407	96032297	96032419
ENSE00003475496	96021946	96022275
ENSE00003476053	96031261	96031334
ENSE00003486994	96022958	96023023
ENSE00003520678	96032033	96032146
ENSE00003523199	96024773	96024843
ENSE00003544981	96022668	96022723
ENSE00003552049	96024189	96024337
ENSE00003555970	96025930	96026012
ENSE00003579999	96023106	96023226
ENSE00003580231	96025485	96025603
ENSE00003598552	96026697	96026909
ENSE00003630845	96030744	96030848
ENSE00003654860	96023923	96024000
ENSE00003655206	96030406	96030534
ENSE00003661697	96023309	96023440
ENSE00003926153	96024427	96024685
ENSE00003988991	96027991	96028090
ENSE00003988994	96027419	96027552

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 90.30.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
apex of heart	UBERON:0002098	90.30	gold quality
right testis	UBERON:0004534	83.86	gold quality
heart left ventricle	UBERON:0002084	82.99	gold quality
left testis	UBERON:0004533	82.61	gold quality
testis	UBERON:0000473	82.35	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	81.52	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.73	gold quality
omental fat pad	UBERON:0010414	80.30	gold quality
adipose tissue	UBERON:0001013	78.28	gold quality
gastrocnemius	UBERON:0001388	77.47	gold quality
lower esophagus muscularis layer	UBERON:0035833	77.31	gold quality
heart	UBERON:0000948	77.27	gold quality
lower esophagus	UBERON:0013473	77.21	gold quality
muscle of leg	UBERON:0001383	76.99	gold quality
hindlimb stylopod muscle	UBERON:0004252	76.86	gold quality
spleen	UBERON:0002106	76.65	gold quality
subcutaneous adipose tissue	UBERON:0002190	76.57	gold quality
thoracic mammary gland	UBERON:0005200	76.06	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	75.33	gold quality
right coronary artery	UBERON:0001625	75.17	gold quality
caudate nucleus	UBERON:0001873	74.92	gold quality
left coronary artery	UBERON:0001626	74.00	gold quality
putamen	UBERON:0001874	73.95	gold quality
left uterine tube	UBERON:0001303	73.69	gold quality
tibial nerve	UBERON:0001323	73.56	gold quality
fundus of stomach	UBERON:0001160	73.54	gold quality
mucosa of stomach	UBERON:0001199	73.50	gold quality
muscle tissue	UBERON:0002385	73.49	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	73.42	gold quality
skeletal muscle tissue	UBERON:0001134	73.36	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-10855	yes	323.63
E-ANND-3	yes	7.96
E-CURD-7	no	61.39
E-ENAD-21	no	61.39

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

15 targeting GPAT2, 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-4283	100.00	66.42	2097
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-4668-5P	99.79	70.58	3782
HSA-MIR-646	99.68	67.84	1645
HSA-MIR-5584-5P	99.49	68.22	2814
HSA-MIR-7515	99.31	68.22	1795
HSA-MIR-149-5P	99.25	67.16	1315
HSA-MIR-3154	98.94	66.55	1455
HSA-MIR-4700-5P	98.63	67.43	1915
HSA-MIR-8089	97.74	66.21	1698
HSA-MIR-4667-5P	97.61	66.67	1683
HSA-MIR-2278	97.30	66.19	1130

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 32.1% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

• GPAT2 as a cancer testis gene (PMID:24967918)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	gpat2	ENSDARG00000053575
mus_musculus	Gpat2	ENSMUSG00000046338
rattus_norvegicus	Gpat2	ENSRNOG00000013906
drosophila_melanogaster	mino	FBGN0027579
caenorhabditis_elegans		WBGENE00017261

Paralogs (2): GNPAT (ENSG00000116906), GPAM (ENSG00000119927)

Protein

Protein identifiers

Glycerol-3-phosphate acyltransferase 2, mitochondrial — Q6NUI2 (reviewed: Q6NUI2)

Alternative names: 1-acylglycerol-3-phosphate O-acyltransferase GPAT2, xGPAT1

All UniProt accessions (3): C9JYV5, Q6NUI2, E9PE95

UniProt curated annotations — full annotation on UniProt →

Function. Transfers an acyl-group from acyl-ACP to the sn-1 position of glycerol-3-phosphate producing a lysophosphatidic acid (LPA), an essential step for the triacylglycerol (TAG) and glycerophospholipids. In vitro also transfers an acyl-group from acyl-ACP to the LPA producing a phosphatidic acid (PA). Prefers arachidonoyl-CoA as the acyl donor. Required for primary processing step during piRNA biosynthesis. Molecular mechanisms by which it promotes piRNA biosynthesis are unclear and do not involve its acyltransferase activity.

Subunit / interactions. Interacts with PIWIL2.

Subcellular location. Mitochondrion outer membrane.

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

Similarity. Belongs to the GPAT/DAPAT family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q6NUI2-1	1	yes
Q6NUI2-3	2
Q6NUI2-4	3
Q6NUI2-5	4

RefSeq proteins (11): NP_001308454, NP_001308455, NP_001308456, NP_001308457, NP_001308458, NP_001308459, NP_001308460, NP_001376568, NP_001409107, NP_001409108, NP_997211 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002123	Plipid/glycerol_acylTrfase	Domain
IPR022284	GPAT/DHAPAT	Family
IPR041728	GPAT/DHAPAT_LPLAT	Domain
IPR045520	GPAT/DHAPAT_C	Domain

Pfam: PF19277

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), 5 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-(9Z-octadecenoyl)-sn-glycero-3-phosphate + (9Z)-octadecenoyl-CoA = 1,2-di-(9Z-octadecenoyl)-sn-glycero-3-phosphate + CoA (RHEA:37131)
• 1-(9Z-octadecenoyl)-sn-glycero-3-phosphate + (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA = 1-(9Z)-octadecenoyl-2-(5Z,8Z,11Z,14Z)-eicosatetraenoyl-sn-glycero-3-phosphate + CoA (RHEA:37443)
• (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA + sn-glycerol 3-phosphate = 1-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phosphate + CoA (RHEA:37463)

UniProt features (21 total): splice variant 5, modified residue 4, topological domain 3, sequence conflict 2, transmembrane region 2, region of interest 2, chain 1, short sequence motif 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6NUI2-F1	78.38	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.

Post-translational modifications (4): 656, 660, 662, 664

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-1483166	Synthesis of PA
R-HSA-75109	Triglyceride biosynthesis

MSigDB gene sets: 75 (showing top): E2F_Q4, E2F_Q4_01, GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_PHOSPHOLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, E2F_Q3, GOCC_MITOCHONDRIAL_ENVELOPE, GOBP_GLYCEROLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROPHOSPHOLIPID_METABOLIC_PROCESS, GOZGIT_ESR1_TARGETS_UP, GOBP_NEUTRAL_LIPID_BIOSYNTHETIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS

GO Biological Process (8): glycerol-3-phosphate metabolic process (GO:0006072), glycerophospholipid metabolic process (GO:0006650), phosphatidic acid biosynthetic process (GO:0006654), CDP-diacylglycerol biosynthetic process (GO:0016024), triglyceride biosynthetic process (GO:0019432), piRNA processing (GO:0034587), lipid metabolic process (GO:0006629), phospholipid biosynthetic process (GO:0008654)

GO Molecular Function (5): 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)

GO Cellular Component (3): mitochondrion (GO:0005739), mitochondrial outer membrane (GO:0005741), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Glycerophospholipid biosynthesis	1
Triglyceride metabolism	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
phospholipid metabolic process	2
glycerophospholipid biosynthetic process	2
alditol phosphate metabolic process	1
glycerolipid metabolic process	1
phosphatidic acid metabolic process	1
CDP-diacylglycerol metabolic process	1
triglyceride metabolic process	1
acylglycerol biosynthetic process	1
regulatory ncRNA processing	1
primary 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
cytoplasm	1
intracellular membrane-bounded organelle	1
mitochondrial membrane	1
organelle outer membrane	1
cellular anatomical structure	1

Protein interactions and networks

STRING

808 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GPAT2	GPAT3	Q53EU6	789
GPAT2	GPAT4	Q86UL3	761
GPAT2	AGPAT5	Q9NUQ2	653
GPAT2	AGPAT4	Q9NRZ5	613
GPAT2	AGPAT1	Q99943	609
GPAT2	AGPAT2	O15120	596
GPAT2	PLD6	Q8N2A8	543
GPAT2	MTHFSD	Q2M296	532
GPAT2	LPCAT2	Q7L5N7	502
GPAT2	DGAT2	Q96PD7	493
GPAT2	AGPAT3	Q9NRZ7	479
GPAT2	DGAT1	O75907	476
GPAT2	TDRD9	Q8NDG6	461
GPAT2	LPCAT4	Q643R3	453
GPAT2	SIRAL2	Q9NWS6	439

IntAct

34 interactions, top by confidence:

A	B	Type	Score
NME3	NME4	psi-mi:“MI:0914”(association)	0.640
PON2	NPC1	psi-mi:“MI:0914”(association)	0.530
TRAK2	OGT	psi-mi:“MI:0914”(association)	0.530
GPAT2	BAG5	psi-mi:“MI:0915”(physical association)	0.400
GPR182	SLC12A8	psi-mi:“MI:0914”(association)	0.350
KLHL34	IFT56	psi-mi:“MI:0914”(association)	0.350
NPAS1	CIBAR1	psi-mi:“MI:0914”(association)	0.350
LDLRAD1	ZNF316	psi-mi:“MI:0914”(association)	0.350
PLEKHG7	MROH6	psi-mi:“MI:0914”(association)	0.350
EEF1AKMT3	SMCHD1	psi-mi:“MI:0914”(association)	0.350
UBXN6	ZSWIM8	psi-mi:“MI:0914”(association)	0.350
D2HGDH	ZSWIM8	psi-mi:“MI:0914”(association)	0.350
PLBD1	ZSWIM8	psi-mi:“MI:0914”(association)	0.350
SULT1C4	ZSWIM8	psi-mi:“MI:0914”(association)	0.350
UPP1	A2ML1	psi-mi:“MI:0914”(association)	0.350
CIAO2A		psi-mi:“MI:0914”(association)	0.350
F12		psi-mi:“MI:0914”(association)	0.350
NT5DC1	ACACB	psi-mi:“MI:0914”(association)	0.350
NT5C	APAF1	psi-mi:“MI:0914”(association)	0.350
CIB2	APAF1	psi-mi:“MI:0914”(association)	0.350
TUSC2	HGS	psi-mi:“MI:0914”(association)	0.350
TMPRSS5	CLGN	psi-mi:“MI:0914”(association)	0.350
REC8	PRORP	psi-mi:“MI:0914”(association)	0.350
DHFR	FANCA	psi-mi:“MI:0914”(association)	0.350
PUS7	PEX1	psi-mi:“MI:0914”(association)	0.350
TLCD3A	ADCY3	psi-mi:“MI:0914”(association)	0.350
MGRN1	NMT2	psi-mi:“MI:0914”(association)	0.350
TRPV5	HNRNPCL1	psi-mi:“MI:0914”(association)	0.350
MEI1	PMPCB	psi-mi:“MI:0914”(association)	0.350
PPTC7	MAOB	psi-mi:“MI:0914”(association)	0.350

BioGRID (34): HSP90AB3P (Affinity Capture-MS), BAG5 (Affinity Capture-MS), GPAT2 (Affinity Capture-MS), GPAT2 (Affinity Capture-MS), GPAT2 (Affinity Capture-MS), GPAT2 (Affinity Capture-MS), GPAT2 (Affinity Capture-MS), GPAT2 (Affinity Capture-MS), GPAT2 (Affinity Capture-MS), GPAT2 (Affinity Capture-MS), GPAT2 (Affinity Capture-MS), GPAT2 (Affinity Capture-MS), GPAT2 (Affinity Capture-MS), GPAT2 (Affinity Capture-MS), GPAT2 (Affinity Capture-MS)

ESM2 similar proteins: A0JNQ6, A6NC42, A6NGQ2, A6NGR9, A6QP75, A7E3N7, A9X185, E1BDF2, E9PGG2, F6SZT2, P0C7A0, P85965, Q06VW1, Q0ZFW8, Q14DK4, Q3UK37, Q3UV16, Q3ZBN4, Q400G9, Q4VXA5, Q587J8, Q5JSQ8, Q60953, Q60I26, Q60I27, Q6NUI2, Q6ZUX3, Q810I0, Q8BH06, Q8C0R7, Q8IWB1, Q8IWY9, Q8IYX4, Q8K4C2, Q8N6L0, Q8N7F7, Q8NCV1, Q8TE82, Q91WA6, Q95JV3

Diamond homologs: D3ZI76, F1S5L4, P97564, Q14DK4, Q5GJ77, Q61586, Q6NUI2, Q9HCL2, A1AIL8, A1JRU2, A3QIU8, A4IF87, A4TRU7, A4W5F4, A5F4F5, A6TGV0, A6VQ68, A7FN98, A7ZUR3, A8A7E1, A8GKB6, A9MGP8, A9N1L4, B1IUL1, B1JNE5, B1LPK6, B1XC40, B2K1U5, B2TX75, B4T1T0, B4TDL8, B4TQQ3, B5BJV8, B5F1Q4, B5FQQ9, B5QZ60, B5R7T4, B5XXZ1, B5Z182, B6ENU1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	3
Uncertain significance	103
Likely benign	11
Benign	2

Top pathogenic / likely-pathogenic (3)

Variant ID	HGVS	Classification
3024503	NM_001321527.2(GPAT2):c.1156-1G>A	Likely pathogenic
3024509	NM_001321527.2(GPAT2):c.1954C>T (p.Arg652Ter)	Likely pathogenic
3024512	NM_001321527.2(GPAT2):c.1879C>T (p.Arg627Trp)	Likely pathogenic

SpliceAI

3812 predictions. Top by Δscore:

Variant	Effect	Δscore
2:96022666:ACC:A	donor_gain	1.0000
2:96022667:CCC:C	donor_gain	1.0000
2:96022720:CACT:C	acceptor_gain	1.0000
2:96022722:CT:C	acceptor_gain	1.0000
2:96022724:C:CC	acceptor_gain	1.0000
2:96022951:GACTC:G	donor_loss	1.0000
2:96022952:ACTC:A	donor_loss	1.0000
2:96022953:CTCA:C	donor_loss	1.0000
2:96022954:TCA:T	donor_loss	1.0000
2:96022955:CA:C	donor_loss	1.0000
2:96022956:A:AC	donor_gain	1.0000
2:96022956:A:C	donor_loss	1.0000
2:96022957:C:CC	donor_gain	1.0000
2:96022957:C:CG	donor_loss	1.0000
2:96022972:T:TA	donor_gain	1.0000
2:96023019:CAACT:C	acceptor_gain	1.0000
2:96023022:CT:C	acceptor_gain	1.0000
2:96023181:G:T	acceptor_gain	1.0000
2:96024334:CAGG:C	acceptor_gain	1.0000
2:96024338:C:CC	acceptor_gain	1.0000
2:96024422:CTCA:C	donor_loss	1.0000
2:96024423:TCAC:T	donor_loss	1.0000
2:96024424:CACC:C	donor_loss	1.0000
2:96024425:A:T	donor_loss	1.0000
2:96024425:ACCG:A	donor_gain	1.0000
2:96024425:ACCGC:A	donor_gain	1.0000
2:96024426:C:CT	donor_loss	1.0000
2:96024426:CCG:C	donor_gain	1.0000
2:96024426:CCGC:C	donor_gain	1.0000
2:96024426:CCGCC:C	donor_gain	1.0000

AlphaMissense

5143 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:96024605:G:C	F497L	0.995
2:96024605:G:T	F497L	0.995
2:96024607:A:G	F497L	0.995
2:96023954:A:G	L622P	0.989
2:96032036:G:C	S58R	0.989
2:96032036:G:T	S58R	0.989
2:96032038:T:G	S58R	0.989
2:96024430:C:G	G556R	0.988
2:96024429:C:T	G556D	0.986
2:96032080:G:T	R44S	0.985
2:96024815:G:C	S462R	0.981
2:96024815:G:T	S462R	0.981
2:96024817:T:G	S462R	0.981
2:96032059:A:G	C51R	0.981
2:96024436:C:G	A554P	0.980
2:96024606:A:G	F497S	0.978
2:96026192:A:C	F382L	0.977
2:96026192:A:T	F382L	0.977
2:96026194:A:G	F382L	0.977
2:96031296:G:C	F72L	0.977
2:96031296:G:T	F72L	0.977
2:96031298:A:G	F72L	0.977
2:96022171:G:C	F792L	0.975
2:96022171:G:T	F792L	0.975
2:96022173:A:G	F792L	0.975
2:96024624:C:G	R491P	0.975
2:96024331:G:T	A559E	0.974
2:96024332:C:G	A559P	0.974
2:96030838:A:G	W88R	0.974
2:96030838:A:T	W88R	0.974

dbSNP variants (sampled 300 via entrez): RS1000587371 (2:97081672 C>T), RS1001913890 (2:96032550 C>G), RS1001984675 (2:97081093 G>A), RS1002035279 (2:97081228 G>A,C), RS1002643577 (2:96025355 A>C), RS1002939352 (2:96025070 C>G), RS1003530833 (2:96026411 C>A), RS1003660610 (2:97079369 A>G), RS1003711537 (2:97079789 C>T), RS1004052218 (2:96028888 A>G), RS1004673028 (2:97079295 A>C), RS1005163503 (2:96025807 C>T), RS1005725021 (2:97082764 A>G), RS1006553392 (2:97082183 C>T), RS1006601374 (2:96023383 G>C,T)

Disease associations

OMIM: gene MIM:616431 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): male infertility (MONDO:0005372)

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST004280_91	Diastolic blood pressure	5.000000e-12

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0006336	diastolic blood pressure

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D007248	Infertility, Male	C12.100.500.430; C12.100.750.700; C12.200.294.430

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
cinnabarinic acid	decreases reaction, increases expression	1
GSK-J4	decreases expression	1
mono-(2-ethylhexyl)phthalate	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment, decreases expression	1
tebuconazole	decreases expression	1
Lipopolysaccharides	increases expression, affects cotreatment, decreases expression, affects response to substance	1
Nickel	increases expression	1
Valproic Acid	increases methylation	1
Oleic Acid	decreases reaction, increases expression	1
Palmitic Acid	decreases reaction, increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT02202382	PHASE4	COMPLETED	Effects of Korean Red Ginseng on Male Infertility
NCT02204826	PHASE4	COMPLETED	Effects of Korean Red Ginseng on Semen Parameters in Male Infertility Patients: a Randomized, Placebo-controlled, Double-blind Clinical Study
NCT03802864	PHASE4	COMPLETED	Post-operative Pain Control of Testicular Sperm Extraction Using Liposomal Bupivacaine
NCT06100432	PHASE4	ACTIVE_NOT_RECRUITING	Effect of Eurycoma Longifolia (DLBS5055) and Multivitamins (Vitamin C+Vitamin E+ β-carotene) for Infertile Males
NCT07523022	PHASE4	ENROLLING_BY_INVITATION	Comparison of the Effect of Gonadotropin and Clomiphene Citrate Treatment on Sperm Parameters and the Outcome of Assisted Reproductive Procedures in Subfertile Men Based on the APHRODITE Groups
NCT00975117	PHASE3	COMPLETED	Spermotrend in the Treatment of Male Infertility
NCT01407432	PHASE3	COMPLETED	Impact of Folates in the Care of the Male Infertility
NCT01895816	PHASE3	COMPLETED	Herbal Tonic Fertile Supplement(ZO2C5)
NCT02605070	PHASE3	TERMINATED	Pilot Study on the Effects of FSH Treatment on the Epigenetic Characteristics of Spermatozoa in Infertile Patients With Severe Oligozoospermia
NCT07402759	PHASE3	ACTIVE_NOT_RECRUITING	Impact of tdrd9 Gene Mutations in the Therapeutic Response to L-carnitine in Oligoasthenozoospermic Men
NCT01880086	PHASE2	COMPLETED	Clomiphene Citrate for the Treatment of Low Testosterone Associated With Chronic Opioid Pain Medication Administration
NCT02061384	PHASE2	COMPLETED	RA-2 13-cis Retinoic Acid (Isotretinoin)
NCT02421887	PHASE2	COMPLETED	Males, Antioxidants, and Infertility Trial
NCT05200663	PHASE2	UNKNOWN	Efficacy Comparison of Tamoxifen and Tamoxifen With Antioxidants on Semen Quality of Male With Idiopathic Infertility
NCT05290558	PHASE2	ACTIVE_NOT_RECRUITING	The Therapeutic Effects of Bu Shen Yi Jing Pill on Semen Quality in Sub Fertile Males: a Randomized Controlled Trial
NCT06091969	PHASE2	NOT_YET_RECRUITING	Supplementation for Male Subfertility
NCT01595308	PHASE1	COMPLETED	A Pilot Study to Evaluate the Effect of Pomegranate Juice on Semen Parameters in Healthy Male Volunteers
NCT02122211	PHASE1	COMPLETED	Choline Dehydrogenase and Sperm Function: Effects of Betaine
NCT02575924	PHASE1	UNKNOWN	Influence of Culture Media on Clinical Outcomes in Poor Responders or Severe Male Infertility
NCT01304927	PHASE2/PHASE3	COMPLETED	Vitamin D Supplementation and Male Infertility: The CBG-study a Randomized Clinical Trial
NCT02349945	PHASE2/PHASE3	COMPLETED	FSH Receptor Polymorphism p.N680S and Efficacy of FSH Therapy
NCT05222841	PHASE2/PHASE3	COMPLETED	The Effectiveness of Spermotrend Food Supplement in the Treatment of Male Infertility
NCT05616598	PHASE2/PHASE3	COMPLETED	Effect of New Oral Treatment for Hepatitis C Virus on Seminal Parameters
NCT02025270	PHASE1/PHASE2	COMPLETED	MSCs For Treatment of Azoospermic Patients
NCT04541459	EARLY_PHASE1	UNKNOWN	Validation of New Devices Against Ambient Electromagnetic Radiation
NCT05792813	EARLY_PHASE1	UNKNOWN	Efficacy and Safety of Linggui Yangyuan Paste in Patients With Male Infertility
NCT06188936	EARLY_PHASE1	COMPLETED	Home Semen Analysis Tests As a Screening Tool for Fertility Patients
NCT00012480	Not specified	COMPLETED	Effect of Environmental Exposures on the Egg Fertilizing Ability of Human Sperm
NCT00044369	Not specified	COMPLETED	Role of the Toxic Metal Cadmium in the Mechanism Producing Infertility With a Varicocele
NCT00119925	Not specified	UNKNOWN	‘SPRING’-Study: Subfertility Guidelines: Patient Related Implementation in the Netherlands Among Gynaecologists
NCT00178516	Not specified	COMPLETED	Vitamin E and Male Infertility
NCT00315029	Not specified	COMPLETED	Patient-Centered Implementation Trial for Single Embryo Transfer
NCT00341120	Not specified	COMPLETED	Genetic Causes of Male Infertility
NCT00481403	Not specified	COMPLETED	Study of Sperm Molecular Factors Implicated in Male Fertility
NCT00548977	Not specified	COMPLETED	Genetic Studies Spermatogenic Failure
NCT00596739	Not specified	COMPLETED	A Study of the Pre- and Post-operative Semen Analyses and Reproductive Hormone Levels of Men Undergoing Weight-reduction Surgery
NCT00756561	Not specified	COMPLETED	HOP-2A - Intratesticular Hormone Levels
NCT00961558	Not specified	TERMINATED	Canadian Varicocelectomy Initiative (CVI): Effects on Male Fertility and Testicular Function of Varicocelectomy
NCT01075334	Not specified	UNKNOWN	Is a Carnitine Based Food Supplement (PorimoreTM) for Infertile Men Superior to Folate and Zinc With Regard to Pregnancy Rates in Intrauterine Insemination Cycles?
NCT01178463	Not specified	UNKNOWN	Spermatogonial Stem Cells in Azoospermic Patients: a Comparison Between Obstructive and Non-obstructive Azoospermia