CHPT1

Summary

CHPT1 (choline phosphotransferase 1, HGNC:17852) is a protein-coding gene on chromosome 12q23.2, encoding Cholinephosphotransferase 1 (Q8WUD6). Catalyzes the final step of de novo phosphatidylcholine (PC) synthesis, i.e. the transfer of choline phosphate from CDP-choline to the free hydroxyl of a diacylglycerol (DAG), producing a PC.

Enables diacylglycerol cholinephosphotransferase activity. Involved in phosphatidylcholine biosynthetic process and platelet activating factor biosynthetic process. Is active in Golgi membrane.

Source: NCBI Gene 56994 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 65 total
• MANE Select transcript: NM_020244

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17852
Approved symbol	CHPT1
Name	choline phosphotransferase 1
Location	12q23.2
Locus type	gene with protein product
Status	Approved
Aliases	CPT1
Ensembl gene	ENSG00000111666
Ensembl biotype	protein_coding
OMIM	616747
Entrez	56994

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 12 protein_coding, 5 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000229266, ENST00000546490, ENST00000546873, ENST00000549128, ENST00000549872, ENST00000550385, ENST00000552213, ENST00000552215, ENST00000552329, ENST00000552351, ENST00000868502, ENST00000868503, ENST00000868504, ENST00000868505, ENST00000868506, ENST00000868507, ENST00000868508, ENST00000868509, ENST00000868510, ENST00000931424

RefSeq mRNA: 1 — MANE Select: NM_020244 NM_020244

CCDS: CCDS9086

Canonical transcript exons

ENST00000229266 — 9 exons

Exon	Start	End
ENSE00001279285	101697640	101698134
ENSE00001330747	101728901	101729074
ENSE00003463439	101714504	101714645
ENSE00003547735	101726294	101726404
ENSE00003565884	101723722	101723847
ENSE00003627795	101720123	101720254
ENSE00003671719	101723168	101723326
ENSE00003672502	101714090	101714237
ENSE00003681037	101716728	101716812

Expression profiles

Bgee: expression breadth ubiquitous, 290 present calls, max score 98.73.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 36.3428 / max 289.2344, expressed in 1811 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
127643	34.3247	1809
127642	0.8608	422
127646	0.3983	220
127645	0.3106	126
127647	0.2762	149
127644	0.1356	49
127641	0.0366	11

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
jejunal mucosa	UBERON:0000399	98.73	gold quality
parotid gland	UBERON:0001831	98.63	gold quality
heart right ventricle	UBERON:0002080	98.60	gold quality
sperm	CL:0000019	97.98	gold quality
male germ cell	CL:0000015	97.87	gold quality
adult organism	UBERON:0007023	97.58	gold quality
right lung	UBERON:0002167	97.56	gold quality
saliva-secreting gland	UBERON:0001044	97.33	gold quality
trabecular bone tissue	UBERON:0002483	97.33	gold quality
right atrium auricular region	UBERON:0006631	97.30	gold quality
minor salivary gland	UBERON:0001830	96.97	gold quality
cardiac ventricle	UBERON:0002082	96.92	gold quality
heart left ventricle	UBERON:0002084	96.92	gold quality
duodenum	UBERON:0002114	96.83	gold quality
corpus epididymis	UBERON:0004359	96.64	gold quality
calcaneal tendon	UBERON:0003701	96.59	gold quality
colonic mucosa	UBERON:0000317	96.56	gold quality
left testis	UBERON:0004533	96.50	gold quality
seminal vesicle	UBERON:0000998	96.49	gold quality
right testis	UBERON:0004534	96.46	gold quality
tibial nerve	UBERON:0001323	96.45	gold quality
lower lobe of lung	UBERON:0008949	96.42	gold quality
nephron tubule	UBERON:0001231	96.33	gold quality
mucosa of sigmoid colon	UBERON:0004993	96.26	gold quality
rectum	UBERON:0001052	96.20	gold quality
liver	UBERON:0002107	96.20	gold quality
heart	UBERON:0000948	96.17	gold quality
apex of heart	UBERON:0002098	96.13	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	96.08	gold quality
mammary duct	UBERON:0001765	96.05	gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	63.99
E-HCAD-1	yes	13.68
E-MTAB-9221	yes	11.43
E-GEOD-75367	no	463.72
E-HCAD-10	no	2.17
E-MTAB-9467	no	1.56
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting CHPT1, 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-548C-3P	99.99	74.01	7587
HSA-MIR-9718	99.94	68.91	918
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-451B	99.55	68.28	1380
HSA-MIR-889-3P	99.40	69.76	2103
HSA-MIR-3908	98.75	67.31	1160
HSA-MIR-628-5P	98.36	67.74	844
HSA-MIR-331-5P	96.59	67.94	705

Literature-anchored findings (GeneRIF, showing 4)

• Furthermore, the activity of CPT in forming PC is increased in the breast cancer cell lines cultured for 24 h. (PMID:15936720)
• Data suggest that PAF-CPT level in blood can be altered by diet; up-regulation of PAF-CPT is associated with diets high in fat and cholesterol; down-regulation of PAF-CPT is associated with healthy diet patterns of the population studied in Greece. (PMID:24639073)
• Genetic Polymorphisms of LPCAT1, CHPT1 and PCYT1B and Risk of Neonatal Respiratory Distress Syndrome among a Chinese Han Population. (PMID:31964590)
• Aberrant activation of super enhancer and choline metabolism drive antiandrogen therapy resistance in prostate cancer. (PMID:32917955)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	chpt1	ENSDARG00000014572
mus_musculus	Chpt1	ENSMUSG00000060002
rattus_norvegicus	Chpt1	ENSRNOG00000058271
drosophila_melanogaster	bbc	FBGN0033844
caenorhabditis_elegans		WBGENE00009057
caenorhabditis_elegans		WBGENE00013024

Paralogs (2): CEPT1 (ENSG00000134255), SELENOI (ENSG00000138018)

Protein

Protein identifiers

Cholinephosphotransferase 1 — Q8WUD6 (reviewed: Q8WUD6)

Alternative names: AAPT1-like protein, Diacylglycerol cholinephosphotransferase 1

All UniProt accessions (5): Q8WUD6, F8W1B3, H0YHV7, H0YI24, H0YI84

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the final step of de novo phosphatidylcholine (PC) synthesis, i.e. the transfer of choline phosphate from CDP-choline to the free hydroxyl of a diacylglycerol (DAG), producing a PC. It thereby plays a central role in the formation and maintenance of vesicular membranes.

Subcellular location. Golgi apparatus membrane.

Tissue specificity. Highly expressed in testis, colon, small intestine, heart, prostate and spleen. Also detected in kidney, skeletal muscle, pancreas, leukocytes, ovary and thymus. Weakly expressed in the brain, placenta and lung. Overexpressed in cancerous breast epithelial cell lines.

Pathway. Phospholipid metabolism; phosphatidylcholine biosynthesis; phosphatidylcholine from phosphocholine: step 2/2.

Similarity. Belongs to the CDP-alcohol phosphatidyltransferase class-I family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8WUD6-1	1, Alpha	yes
Q8WUD6-2	2, Beta

RefSeq proteins (1): NP_064629* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000462	CDP-OH_P_trans	Family
IPR014472	CHOPT	Family
IPR043130	CDP-OH_PTrfase_TM_dom	Homologous_superfamily
IPR048254	CDP_ALCOHOL_P_TRANSF_CS	Conserved_site

Pfam: PF01066

Enzyme classification (BRENDA):

• EC 2.7.8.2 — diacylglycerol cholinephosphotransferase (BRENDA: 34 organisms, 101 substrates, 94 inhibitors, 36 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

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

Substrate	Km (mM)	Measurements
CDP-CHOLINE	0.0166–0.53	8
1,2-DIOLEOYL-SN-GLYCEROL	0.0509–0.12	2
CDP-ETHANOLAMINE	0.098–0.101	2
1-ARACHIDOYL-2-OLEOYL-SN-GLYCEROL	0.16	1
1-HEPTADECANOYL-2-OLEOYL-SN-GLYCEROL	0.17	1
1-HEXADECANOYL-2-OCTADECANOYL-SN-GLYCEROL	0.0143	1
1-HEXADECYL-2-OCTADECENOYL-SN-GLYCEROL	0.0262	1
1-LAUROYL-2-OLEOYL-SN-GLYCEROL	0.133	1
1-MYRISTOYL-2-OLEOYL-SN-GLYCEROL	0.104	1
1-NONADECANOYL-2-OLEOYL-SN-GLYCEROL	0.21	1
1-O-ALKYL-2-ACETYL-SN-GLYCEROL	0.0593	1
1-PALMITOYL-2-OLEOYL-SN-GLYCEROL	0.116	1
1-PENTADECANOYL-2-OLEOYL-SN-GLYCEROL	0.109	1
1-TRIDECANOYL-2-OLEOYL-SN-GLYCEROL	0.122	1
BACTERIAL 1,2-DIACYL-SN-GLYCEROL	0.0405	1

Catalyzed reactions (Rhea), 5 shown:

• CDP-choline + a 1,2-diacyl-sn-glycerol = a 1,2-diacyl-sn-glycero-3-phosphocholine + CMP + H(+) (RHEA:32939)
• 1,2-dioctanoyl-sn-glycerol + CDP-choline = 1,2-dioctanoyl-sn-glycero-3-phosphocholine + CMP + H(+) (RHEA:54232)
• 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycerol + CDP-choline = 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine + CMP + H(+) (RHEA:54244)
• 1-hexadecanoyl-2-(4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl)-sn-glycerol + CDP-choline = 1-hexadecanoyl-2-(4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl)-sn-glycero-3-phosphocholine + CMP + H(+) (RHEA:54332)
• 1-octadecanoyl-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycerol + CDP-choline = 1-octadecanoyl-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phosphocholine + CMP + H(+) (RHEA:54344)

UniProt features (42 total): topological domain 11, transmembrane region 10, binding site 8, sequence conflict 4, splice variant 2, sequence variant 2, initiator methionine 1, chain 1, active site 1, site 1, modified residue 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
9UET	ELECTRON MICROSCOPY	3.68

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WUD6-F1	91.30	0.87

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (2): 133 (proton acceptor); 129 (increases basicity of active site his)

Ligand- & substrate-binding residues (8): 64; 111; 111; 114; 119; 132; 132; 136

Post-translational modifications (1): 2

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-1483191	Synthesis of PC

MSigDB gene sets: 226 (showing top): GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLCHOLINE_METABOLIC_PROCESS, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GOBP_PHOSPHATIDYLCHOLINE_BIOSYNTHETIC_PROCESS, GOLDRATH_IMMUNE_MEMORY, GOBP_GROWTH, DARWICHE_SKIN_TUMOR_PROMOTER_UP, DARWICHE_PAPILLOMA_RISK_LOW_UP, DARWICHE_PAPILLOMA_RISK_HIGH_UP, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, DARWICHE_SQUAMOUS_CELL_CARCINOMA_UP, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_PHOSPHOLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, MARTINEZ_RB1_TARGETS_UP

GO Biological Process (7): regulation of cell growth (GO:0001558), lipid metabolic process (GO:0006629), phosphatidylcholine biosynthetic process (GO:0006656), CDP-choline pathway (GO:0006657), platelet activating factor biosynthetic process (GO:0006663), lipid biosynthetic process (GO:0008610), phospholipid biosynthetic process (GO:0008654)

GO Molecular Function (6): diacylglycerol cholinephosphotransferase activity (GO:0004142), diacylglycerol binding (GO:0019992), metal ion binding (GO:0046872), protein binding (GO:0005515), transferase activity (GO:0016740), phosphotransferase activity, for other substituted phosphate groups (GO:0016780)

GO Cellular Component (7): Golgi membrane (GO:0000139), endoplasmic reticulum membrane (GO:0005789), Golgi apparatus (GO:0005794), membrane (GO:0016020), intracellular membrane-bounded organelle (GO:0043231), cytoplasm (GO:0005737), endomembrane system (GO:0012505)

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
cellular anatomical structure	3
glycerophospholipid biosynthetic process	2
intracellular anatomical structure	2
cell growth	1
regulation of growth	1
regulation of cellular component organization	1
primary metabolic process	1
phosphatidylcholine metabolic process	1
choline kinase activity	1
diacylglycerol cholinephosphotransferase activity	1
phosphatidylcholine biosynthetic process	1
ether lipid biosynthetic process	1
platelet activating factor metabolic process	1
lipid metabolic process	1
biosynthetic process	1
phospholipid metabolic process	1
lipid biosynthetic process	1
organophosphate biosynthetic process	1
CDP-alcohol phosphatidyltransferase activity	1
lipid binding	1
cation binding	1
binding	1
catalytic activity	1
transferase activity, transferring phosphorus-containing groups	1
Golgi apparatus	1
bounding membrane of organelle	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
membrane-bounded organelle	1
intracellular organelle	1
vacuole	1
plasma membrane	1

Protein interactions and networks

STRING

1164 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CHPT1	PCYT1B	Q9Y5K3	795
CHPT1	PCYT1A	P49585	770
CHPT1	CHKA	P35790	729
CHPT1	PEMT	Q9UBM1	714
CHPT1	PCYT2	Q99447	688
CHPT1	CHKB	Q9Y259	653
CHPT1	MBOAT2	Q6ZWT7	644
CHPT1	LPCAT2	Q7L5N7	638
CHPT1	PGS1	Q32NB8	613
CHPT1	LPCAT1	Q8NF37	605
CHPT1	CDIPT	O14735	592
CHPT1	GPCPD1	Q9NPB8	588
CHPT1	LPCAT3	Q6P1A2	576
CHPT1	PISD	Q9UG56	572
CHPT1	ETNK2	Q9NVF9	549

IntAct

85 interactions, top by confidence:

A	B	Type	Score
ENTREP1	WWP2	psi-mi:“MI:0914”(association)	0.850
CFTR	ESYT2	psi-mi:“MI:0914”(association)	0.710
RXYLT1	FKTN	psi-mi:“MI:0914”(association)	0.710
CHPT1	TLCD4	psi-mi:“MI:0915”(physical association)	0.560
SLC39A5	TMEM223	psi-mi:“MI:0914”(association)	0.530
APLNR	METTL15	psi-mi:“MI:0914”(association)	0.530
SLC15A1	METTL15	psi-mi:“MI:0914”(association)	0.530
VASN	AP3B1	psi-mi:“MI:0914”(association)	0.530
CD1B	TOR1B	psi-mi:“MI:0914”(association)	0.530
SPPL2B	UQCRQ	psi-mi:“MI:0914”(association)	0.530
CDH13	INSIG1	psi-mi:“MI:0914”(association)	0.530
TMEM171	THAP12	psi-mi:“MI:0914”(association)	0.530
GPR52	SYNGR2	psi-mi:“MI:0914”(association)	0.530
LRRC8B	SLC25A17	psi-mi:“MI:0914”(association)	0.530
CD70	METTL15	psi-mi:“MI:0914”(association)	0.530
PDCD1	RTL8C	psi-mi:“MI:0914”(association)	0.530
SLC22A9	GPR89A	psi-mi:“MI:0914”(association)	0.530
DGCR2	HOXD13	psi-mi:“MI:0914”(association)	0.530
MEP1B	CHPT1	psi-mi:“MI:0915”(physical association)	0.370
CHPT1	DRD2	psi-mi:“MI:0915”(physical association)	0.370
CHPT1	HTR2B	psi-mi:“MI:0915”(physical association)	0.370
CHPT1	LTB4R2	psi-mi:“MI:0915”(physical association)	0.370
K14	MAP2K7	psi-mi:“MI:0914”(association)	0.350
OCRL	MYO1C	psi-mi:“MI:0914”(association)	0.350

BioGRID (103): CHPT1 (Affinity Capture-MS), CHPT1 (Affinity Capture-MS), CHPT1 (Affinity Capture-MS), CHPT1 (Affinity Capture-MS), CHPT1 (Affinity Capture-MS), CHPT1 (Affinity Capture-MS), CHPT1 (Affinity Capture-MS), CHPT1 (Affinity Capture-MS), CHPT1 (Affinity Capture-MS), CHPT1 (Proximity Label-MS), CHPT1 (Affinity Capture-MS), CHPT1 (Affinity Capture-MS), CHPT1 (Affinity Capture-MS), CHPT1 (Affinity Capture-MS), CHPT1 (Affinity Capture-MS)

ESM2 similar proteins: A2XX73, A3F5L3, A5PJS2, C8VRV0, O05883, O12947, O18765, O60725, O88455, P18405, P24008, P31214, Q08388, Q0II71, Q28891, Q41131, Q4KLV1, Q4V7R2, Q564G3, Q5PRC0, Q61907, Q66H21, Q68FF9, Q6NV38, Q6QHC5, Q6RS95, Q71KT5, Q7S5W9, Q7SXF1, Q7XSR9, Q7YRH6, Q7ZW02, Q7ZXH1, Q84UB8, Q84UB9, Q84UC0, Q8C025, Q8GZC2, Q8L586, Q8R2F2

Diamond homologs: O13901, O82567, O82568, P17898, P22140, Q1LZE6, Q28H54, Q4KLV1, Q54XM0, Q550W1, Q5NV96, Q5ZHQ5, Q5ZKD1, Q66H21, Q6AXM5, Q7ZW02, Q7ZYQ3, Q80TA1, Q8BGS7, Q8C025, Q8T2Q6, Q8WUD6, Q95ZE2, Q9C0D9, Q9Y6K0, Q55AQ3, Q17QM4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 104 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
Peptide ligand-binding receptors	7	8.1×	2e-03
SLC-mediated transmembrane transport	8	7.4×	2e-03
Class A/1 (Rhodopsin-like receptors)	6	7.0×	8e-03
G alpha (i) signalling events	8	4.9×	8e-03

GO biological processes:

GO term	Partners	Fold	FDR
phospholipase C-activating G protein-coupled receptor signaling pathway	7	10.0×	5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	52
Likely benign	1
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

2756 predictions. Top by Δscore:

Variant	Effect	Δscore
12:101714233:CACAG:C	donor_loss	1.0000
12:101714234:ACAG:A	donor_loss	1.0000
12:101714235:CAGG:C	donor_loss	1.0000
12:101714236:AGGTA:A	donor_loss	1.0000
12:101714237:GG:G	donor_loss	1.0000
12:101714238:G:GC	donor_loss	1.0000
12:101714239:T:A	donor_loss	1.0000
12:101716727:GA:G	acceptor_gain	1.0000
12:101720252:GCA:G	donor_gain	1.0000
12:101720255:G:GG	donor_gain	1.0000
12:101723844:AATGG:A	donor_loss	1.0000
12:101723846:TGG:T	donor_loss	1.0000
12:101723847:GGT:G	donor_loss	1.0000
12:101723848:G:GG	donor_gain	1.0000
12:101723848:G:T	donor_loss	1.0000
12:101723849:TAA:T	donor_loss	1.0000
12:101728987:CA:C	acceptor_gain	1.0000
12:101728988:A:C	acceptor_gain	1.0000
12:101729209:ATACT:A	acceptor_gain	1.0000
12:101729210:TACT:T	acceptor_gain	1.0000
12:101729212:CT:C	acceptor_gain	1.0000
12:101729214:C:CC	acceptor_gain	1.0000
12:101729214:CT:C	acceptor_loss	1.0000
12:101731588:A:C	donor_gain	1.0000
12:101731662:ATATT:A	acceptor_gain	1.0000
12:101731663:TATT:T	acceptor_gain	1.0000
12:101731664:ATTC:A	acceptor_loss	1.0000
12:101731665:TT:T	acceptor_gain	1.0000
12:101731665:TTCTA:T	acceptor_loss	1.0000
12:101731666:TC:T	acceptor_loss	1.0000

AlphaMissense

2629 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:101714211:A:C	D132A	0.998
12:101714211:A:T	D132V	0.998
12:101714608:T:A	W176R	0.998
12:101714608:T:C	W176R	0.998
12:101714157:A:T	D114V	0.997
12:101714205:T:C	L130P	0.997
12:101714212:C:A	D132E	0.997
12:101714212:C:G	D132E	0.997
12:101714214:A:C	H133P	0.997
12:101714148:A:C	D111A	0.996
12:101714149:T:A	D111E	0.996
12:101714149:T:G	D111E	0.996
12:101714223:A:C	D136A	0.996
12:101714224:C:A	D136E	0.996
12:101714224:C:G	D136E	0.996
12:101714621:T:A	V180D	0.996
12:101716801:T:A	W213R	0.996
12:101716801:T:C	W213R	0.996
12:101723725:G:C	A315P	0.996
12:101714145:T:C	L110P	0.995
12:101714148:A:T	D111V	0.995
12:101714156:G:C	D114H	0.995
12:101714158:T:A	D114E	0.995
12:101714158:T:G	D114E	0.995
12:101714211:A:G	D132G	0.995
12:101714213:C:G	H133D	0.995
12:101714215:T:A	H133Q	0.995
12:101714215:T:G	H133Q	0.995
12:101714219:T:C	C135R	0.995
12:101714223:A:G	D136G	0.995

dbSNP variants (sampled 300 via entrez): RS1000151246 (12:101696346 A>G), RS1000270199 (12:101726723 T>A,C), RS1000430539 (12:101711817 A>G), RS1000537887 (12:101704360 C>G), RS1000611617 (12:101719071 C>T), RS1000950689 (12:101713719 A>C), RS1000976843 (12:101713379 C>T), RS1000992806 (12:101704560 C>G), RS1001001964 (12:101727964 A>G), RS1001164125 (12:101720561 A>G), RS1001188433 (12:101703717 C>T), RS1001256414 (12:101706223 A>G,T), RS1001258753 (12:101703977 T>C,G), RS1001264387 (12:101728585 C>T), RS1001338902 (12:101713700 A>G)

Disease associations

OMIM: gene MIM:616747 | disease phenotypes: MIM:270960

GenCC curated gene-disease

Mondo (1): spermatogenic failure 4 (MONDO:0010052)

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST010703_2	Brain morphology (MOSTest)	3.000000e-37
GCST011088_8	Orofacial clefts	2.000000e-06
GCST011816_8	Vitamin C levels	6.000000e-20

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement
EFO:0600003	vitamin C measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C536875	Arrest of spermatogenesis (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, decreases methylation	6
trichostatin A	affects cotreatment, increases expression	3
Nickel	decreases expression	3
Benzo(a)pyrene	decreases expression, increases methylation	2
Tretinoin	decreases expression, increases expression	2
Cyclosporine	decreases expression	2
triphenyl phosphate	affects expression	1
beta-lapachone	decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, increases expression	1
2,3-dimethoxy-1,4-naphthoquinone	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
K 7174	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Vorinostat	increases expression	1
Atrazine	increases expression	1
Cadmium	increases activity, increases expression	1
Coumestrol	affects cotreatment, increases expression	1
Estradiol	affects binding, increases expression	1
Lead	affects expression	1
Methyl Methanesulfonate	decreases expression	1
Methylcholanthrene	affects binding, increases reaction	1
Progesterone	increases expression	1
Rotenone	increases expression	1
Thimerosal	increases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tunicamycin	increases expression	1

Clinical trials (associated diseases)

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