EDC3

Summary

EDC3 (enhancer of mRNA decapping 3, HGNC:26114) is a protein-coding gene on chromosome 15q24.1, encoding Enhancer of mRNA-decapping protein 3 (Q96F86). Binds single-stranded RNA.

This gene encodes a protein that is important in mRNA degradation. The encoded protein is a component of a decapping complex that promotes efficient removal of the monomethylguanosine (m7G) cap from mRNAs, as part of the 5’ to 3’ mRNA decay pathway. Mutations in this gene have been identified in human patients with an autosomal recessive form of intellectual disability.

Source: NCBI Gene 80153 — RefSeq curated summary.

At a glance

• Gene–disease (curated): autosomal recessive non-syndromic intellectual disability (Supportive, GenCC) — +1 more curated relationship
• GWAS associations: 18
• Clinical variants (ClinVar): 68 total — 2 pathogenic
• Phenotypes (HPO): 6
• MANE Select transcript: NM_025083

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26114
Approved symbol	EDC3
Name	enhancer of mRNA decapping 3
Location	15q24.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ21128, hYjeF_N2-15q23, YJEFN2, LSM16
Ensembl gene	ENSG00000179151
Ensembl biotype	protein_coding
OMIM	609842
Entrez	80153

Gene structure

Transcript identifiers

Ensembl transcripts: 28 — 24 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000315127, ENST00000426797, ENST00000562047, ENST00000562174, ENST00000562974, ENST00000563009, ENST00000563292, ENST00000565602, ENST00000566119, ENST00000566219, ENST00000566243, ENST00000566828, ENST00000567813, ENST00000568176, ENST00000569007, ENST00000569561, ENST00000569606, ENST00000570138, ENST00000647659, ENST00000875246, ENST00000875247, ENST00000875248, ENST00000875249, ENST00000875250, ENST00000875251, ENST00000934283, ENST00000934284, ENST00000934285

RefSeq mRNA: 5 — MANE Select: NM_025083 NM_001142443, NM_001142444, NM_001351378, NM_001351379, NM_025083

CCDS: CCDS10267

Canonical transcript exons

ENST00000315127 — 7 exons

Exon	Start	End
ENSE00001253676	74671455	74671774
ENSE00001856853	74630558	74632946
ENSE00002583226	74695880	74696024
ENSE00003464012	74635409	74635626
ENSE00003599244	74655733	74656068
ENSE00003648252	74640466	74640619
ENSE00003793240	74674961	74675142

Expression profiles

Bgee: expression breadth ubiquitous, 204 present calls, max score 92.90.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.3690 / max 88.0971, expressed in 1802 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
150925	13.7665	1801
207587	0.6025	322

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	92.90	gold quality
right testis	UBERON:0004534	92.89	gold quality
cortical plate	UBERON:0005343	91.34	gold quality
testis	UBERON:0000473	90.84	gold quality
stromal cell of endometrium	CL:0002255	90.74	gold quality
ganglionic eminence	UBERON:0004023	90.12	gold quality
ventricular zone	UBERON:0003053	89.25	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.84	gold quality
islet of Langerhans	UBERON:0000006	88.25	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	87.76	gold quality
granulocyte	CL:0000094	86.19	gold quality
right lobe of thyroid gland	UBERON:0001119	86.17	gold quality
apex of heart	UBERON:0002098	86.12	gold quality
embryo	UBERON:0000922	86.04	gold quality
right hemisphere of cerebellum	UBERON:0014890	85.79	gold quality
colonic epithelium	UBERON:0000397	85.70	gold quality
cerebellar hemisphere	UBERON:0002245	85.36	gold quality
cerebellar cortex	UBERON:0002129	85.31	gold quality
right ovary	UBERON:0002118	85.17	gold quality
rectum	UBERON:0001052	85.14	gold quality
lower esophagus mucosa	UBERON:0035834	85.11	gold quality
mucosa of transverse colon	UBERON:0004991	85.01	gold quality
left lobe of thyroid gland	UBERON:0001120	85.00	gold quality
body of uterus	UBERON:0009853	84.86	gold quality
monocyte	CL:0000576	84.82	gold quality
leukocyte	CL:0000738	84.74	gold quality
gastrocnemius	UBERON:0001388	84.73	gold quality
esophagus mucosa	UBERON:0002469	84.69	gold quality
mononuclear cell	CL:0000842	84.61	gold quality
left ovary	UBERON:0002119	84.55	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.65

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

92 targeting EDC3, 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-4768-5P	100.00	69.49	2861
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-22-3P	99.93	68.13	917
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-6515-3P	99.82	68.19	1933
HSA-MIR-139-5P	99.80	69.50	1399
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-3175	99.65	66.30	2031

Literature-anchored findings (GeneRIF, showing 5)

• The modular architecture enables EDC3 to interact with multiple components of the decapping machinery, including DCP1, DCP2, and Me31B. (PMID:17923697)
• The dimerization interface of Edc3 is highly conserved in eukaryotes despite the overall low sequence homology across species; structure-based site-directed mutagenesis revealed dimerization is required for efficient RNA binding, P-body formation (PMID:18678652)
• Structural basis for the mutually exclusive anchoring of P body components EDC3 and Tral to the DEAD box protein DDX6/Me31B. (PMID:19285948)
• In vitro decapping assays showed that altered EDC3 is unable to enhance DCP2 decapping at low concentrations and even inhibits DCP2 decapping at high concentration. (PMID:25701870)
• EDC3 might be preferentially involved in the degradation of long coding and non-coding RNAs (PMID:29685133)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	edc3	ENSDARG00000051931
mus_musculus	Edc3	ENSMUSG00000038957
rattus_norvegicus	Edc3	ENSRNOG00000019579
drosophila_melanogaster	Edc3	FBGN0036735
caenorhabditis_elegans	edc-3	WBGENE00011036

Protein

Protein identifiers

Enhancer of mRNA-decapping protein 3 — Q96F86 (reviewed: Q96F86)

Alternative names: LSM16 homolog, YjeF N-terminal domain-containing protein 2, YjeF domain-containing protein 1

All UniProt accessions (13): Q96F86, H3BMB8, H3BNJ7, H3BPN4, H3BPW9, H3BQ37, H3BQA1, H3BQP5, H3BSQ0, H3BTD6, H3BTF8, H3BTH0, H3BU87

UniProt curated annotations — full annotation on UniProt →

Function. Binds single-stranded RNA. Involved in the process of mRNA degradation and in the positive regulation of mRNA decapping. May play a role in spermiogenesis and oogenesis.

Subunit / interactions. Homodimer (via YjeF N-terminal domain). Forms a complex with DCP1A, DCP2, DDX6 and EDC4/HEDLS, within this complex directly interacts with DCP1A and DDX6. Interacts with ZFP36.

Subcellular location. Cytoplasm. P-body.

Tissue specificity. Expressed in theca and granulosa cells in ovary, and in spermatids of the meiotic division part II and apical membrane of Sertoli cells in testis (at protein level). Also expressed in brain and mammary gland.

Disease relevance. Intellectual developmental disorder, autosomal recessive 50 (MRT50) [MIM:616460] A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRT50 patients show mild intellectual disability and microcephaly. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The DFDF domain is unstructured by itself. It assumes a helical fold upon interaction with DDX6.

Similarity. Belongs to the EDC3 family.

RefSeq proteins (5): NP_001135915, NP_001135916, NP_001338307, NP_001338308, NP_079359* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004443	YjeF_N_dom	Domain
IPR019050	FDF_dom	Domain
IPR025609	Lsm14-like_N	Domain
IPR025762	DFDF	Domain
IPR034107	Lsm16_N	Domain
IPR036652	YjeF_N_dom_sf	Homologous_superfamily
IPR047575	Sm	Domain

Pfam: PF03853, PF09532, PF12701, PF16598

UniProt features (49 total): strand 15, helix 12, turn 5, modified residue 4, mutagenesis site 4, domain 3, region of interest 3, chain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

6 structures.

PDB	Method	Resolution (Å)
2VC8	X-RAY DIFFRACTION	1.31
3D3K	X-RAY DIFFRACTION	2.2
6S8S	X-RAY DIFFRACTION	2.21
2WAX	X-RAY DIFFRACTION	2.3
2WAY	X-RAY DIFFRACTION	2.3
3D3J	X-RAY DIFFRACTION	2.8

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96F86-F1	77.04	0.50

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): 161, 131, 138, 140

Mutagenesis-validated functional residues (4):

Position	Phenotype
204	abolishes interaction with ddx6; when associated with a-206.
206	abolishes interaction with ddx6; when associated with a-204.
306	abolishes homodimerization and rna binding; when associated with a-310.
310	abolishes homodimerization and rna binding; when associated with a-306.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-430039	mRNA decay by 5’ to 3’ exoribonuclease

MSigDB gene sets: 124 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, GOBP_P_BODY_ASSEMBLY, GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, XU_GH1_AUTOCRINE_TARGETS_UP, REACTOME_MRNA_DECAY_BY_5_TO_3_EXORIBONUCLEASE, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOBP_REGULATION_OF_CATABOLIC_PROCESS, GOBP_POSITIVE_REGULATION_OF_CATABOLIC_PROCESS, GOBP_ORGANELLE_ASSEMBLY, GOBP_NUCLEAR_TRANSCRIBED_MRNA_CATABOLIC_PROCESS_DEADENYLATION_DEPENDENT_DECAY, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, NRF2_01, REACTOME_METABOLISM_OF_RNA, GOCC_RIBONUCLEOPROTEIN_GRANULE

GO Biological Process (2): deadenylation-independent decapping of nuclear-transcribed mRNA (GO:0031087), P-body assembly (GO:0033962)

GO Molecular Function (4): mRNA binding (GO:0003729), identical protein binding (GO:0042802), RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (5): P-body (GO:0000932), cytosol (GO:0005829), membrane (GO:0016020), cytoplasmic ribonucleoprotein granule (GO:0036464), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Deadenylation-dependent mRNA decay	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
cytoplasm	2
nuclear-transcribed mRNA catabolic process, deadenylation-independent decay	1
mRNA methylguanosine-cap decapping	1
membraneless organelle assembly	1
RNA binding	1
protein binding	1
nucleic acid binding	1
binding	1
cytoplasmic ribonucleoprotein granule	1
ribonucleoprotein granule	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

2136 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
EDC3	XRN1	Q8IZH2	999
EDC3	DCP2	Q8IU60	999
EDC3	DDX6	P26196	999
EDC3	EDC4	Q6P2E9	998
EDC3	LSM1	O15116	991
EDC3	DCP1A	Q9NPI6	988
EDC3	LSM14A	Q8ND56	986
EDC3	PATL1	Q86TB9	893
EDC3	LSM4	Q9Y4Z0	882
EDC3	UPF1	Q92900	866
EDC3	DCP1B	Q8IZD4	833
EDC3	TNRC6A	Q8NDV7	793
EDC3	PABPC1	P11940	788
EDC3	LSM14B	Q9BX40	784
EDC3	RPS28	P25112	760

IntAct

274 interactions, top by confidence:

A	B	Type	Score
EDC3	DDX6	psi-mi:“MI:0914”(association)	0.960
DDX6	EDC3	psi-mi:“MI:0915”(physical association)	0.960
EDC3	DDX6	psi-mi:“MI:0915”(physical association)	0.960
DCP1A	EDC3	psi-mi:“MI:0403”(colocalization)	0.950
EDC3	DCP1A	psi-mi:“MI:0915”(physical association)	0.950
DCP1A	EDC3	psi-mi:“MI:0915”(physical association)	0.950
EDC3	DCP1B	psi-mi:“MI:0915”(physical association)	0.930
DCP1B	EDC3	psi-mi:“MI:0915”(physical association)	0.930
DCP1A	EDC4	psi-mi:“MI:0914”(association)	0.880
EDC3	ANXA10	psi-mi:“MI:0915”(physical association)	0.870
ANXA10	EDC3	psi-mi:“MI:0915”(physical association)	0.870
EDC3	EDC3	psi-mi:“MI:0915”(physical association)	0.870

BioGRID (304): EDC3 (Two-hybrid), EDC3 (Two-hybrid), EDC3 (Two-hybrid), EFHC2 (Two-hybrid), DCP1B (Two-hybrid), EDC3 (Affinity Capture-MS), EDC3 (Affinity Capture-MS), EDC3 (Affinity Capture-MS), EDC3 (Affinity Capture-MS), EDC3 (Affinity Capture-MS), DCP1B (Affinity Capture-MS), DCP1A (Affinity Capture-MS), EDC3 (Affinity Capture-MS), EDC3 (Proximity Label-MS), EDC3 (Proximity Label-MS)

ESM2 similar proteins: A2AFR3, A2VDY6, O94967, P0C606, P79987, Q03353, Q03354, Q03355, Q14161, Q1L8G7, Q3UX43, Q4R8N2, Q4R8V9, Q50H33, Q58A45, Q5RDU9, Q5RED8, Q5TKA1, Q5VUG0, Q5ZL38, Q641K1, Q68CL5, Q6AXS8, Q6GR30, Q6PAJ1, Q6ZWB6, Q7SXV2, Q7ZXY4, Q8C5G2, Q8C735, Q8CB44, Q8CGF6, Q8IWR0, Q8K2D3, Q8N6S4, Q8QFX1, Q8VDD9, Q8WUU5, Q8WWQ0, Q8WXG6

Diamond homologs: Q4R8V9, Q502M5, Q5RDU9, Q5XH48, Q5ZLS2, Q8K2D3, Q96F86, Q9VVI2

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
14-3-3	“down-regulates activity”	EDC3	binding
AKT	“down-regulates activity”	EDC3	phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 133 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
Activation of BAD and translocation to mitochondria	7	55.5×	3e-09
mRNA decay by 5’ to 3’ exoribonuclease	7	55.5×	3e-09
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	7	49.0×	5e-09
SARS-CoV-1 targets host intracellular signalling and regulatory pathways	7	49.0×	5e-09
Activation of BH3-only proteins	7	36.2×	5e-08
Intrinsic Pathway for Apoptosis	8	24.4×	7e-08
RHO GTPases activate PKNs	7	23.1×	1e-06
FOXO-mediated transcription	5	17.5×	2e-04

GO biological processes:

GO term	Partners	Fold	FDR
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	5	19.5×	6e-04
protein targeting	6	18.3×	4e-04
intracellular protein localization	9	7.8×	5e-04
protein phosphorylation	10	5.7×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	44
Likely benign	13
Benign	1

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
3068515	NM_025083.5(EDC3):c.512del (p.Gln171fs)	Pathogenic
372218	NM_025083.5(EDC3):c.161T>C (p.Phe54Ser)	Pathogenic

SpliceAI

1778 predictions. Top by Δscore:

Variant	Effect	Δscore
15:74635622:TCAAC:T	acceptor_gain	1.0000
15:74635623:CAACC:C	acceptor_gain	1.0000
15:74635626:CCTG:C	acceptor_loss	1.0000
15:74635628:T:C	acceptor_loss	1.0000
15:74655726:AACTC:A	donor_loss	1.0000
15:74655727:ACTCA:A	donor_loss	1.0000
15:74655728:CTCAC:C	donor_loss	1.0000
15:74655729:TCA:T	donor_loss	1.0000
15:74655731:A:AC	donor_gain	1.0000
15:74655731:AC:A	donor_gain	1.0000
15:74655732:C:CC	donor_gain	1.0000
15:74655732:CC:C	donor_gain	1.0000
15:74656064:TGACC:T	acceptor_gain	1.0000
15:74656065:GACC:G	acceptor_gain	1.0000
15:74656066:ACCC:A	acceptor_loss	1.0000
15:74656067:CC:C	acceptor_gain	1.0000
15:74656068:CC:C	acceptor_gain	1.0000
15:74656068:CCTG:C	acceptor_loss	1.0000
15:74656069:C:CC	acceptor_gain	1.0000
15:74671449:A:AC	donor_gain	1.0000
15:74671450:C:CC	donor_gain	1.0000
15:74671451:TTA:T	donor_loss	1.0000
15:74671452:TAC:T	donor_loss	1.0000
15:74671453:A:AC	donor_gain	1.0000
15:74671453:ACAGG:A	donor_loss	1.0000
15:74671454:C:CA	donor_gain	1.0000
15:74671454:CA:C	donor_gain	1.0000
15:74671454:CAG:C	donor_gain	1.0000
15:74671454:CAGG:C	donor_gain	1.0000
15:74671454:CAGGA:C	donor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000089853 (15:74680563 T>C), RS1000101298 (15:74655371 T>A,C), RS1000198387 (15:74645344 G>T), RS1000199067 (15:74638024 A>C,G), RS1000219351 (15:74659226 G>A), RS1000312604 (15:74644968 T>A,C), RS1000386061 (15:74698022 A>G), RS1000403258 (15:74652789 A>G), RS1000426138 (15:74652515 A>G), RS1000525838 (15:74660189 T>C), RS1000668228 (15:74631144 C>T), RS1000703505 (15:74653821 A>G), RS1000732298 (15:74652389 G>A), RS1000741169 (15:74631305 C>T), RS1000746279 (15:74685475 G>C)

Disease associations

OMIM: gene MIM:609842 | disease phenotypes: MIM:616460

GenCC curated gene-disease

Disease	Classification	Inheritance
autosomal recessive non-syndromic intellectual disability	Supportive	Autosomal recessive
intellectual disability, autosomal recessive 50	Limited	Autosomal recessive

Mondo (2): intellectual disability, autosomal recessive 50 (MONDO:0014649), autosomal recessive non-syndromic intellectual disability (MONDO:0019502)

Orphanet (1): Autosomal recessive non-syndromic intellectual disability (Orphanet:88616)

HPO phenotypes

6 total (6 of 6 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000252	Microcephaly
HP:0000407	Sensorineural hearing impairment
HP:0001100	Heterochromia iridis
HP:0001256	Mild intellectual disability
HP:0011463	Childhood onset

GWAS associations

18 associations (top):

Study	Trait	p-value
GCST001032_7	Caffeine consumption	5.000000e-14
GCST003846_10	Caffeine metabolism (plasma 1,3,7-trimethylxanthine (caffeine) level)	5.000000e-18
GCST003846_11	Caffeine metabolism (plasma 1,3,7-trimethylxanthine (caffeine) level)	1.000000e-20
GCST003846_7	Caffeine metabolism (plasma 1,3,7-trimethylxanthine (caffeine) level)	1.000000e-11
GCST003846_8	Caffeine metabolism (plasma 1,3,7-trimethylxanthine (caffeine) level)	2.000000e-16
GCST003846_9	Caffeine metabolism (plasma 1,3,7-trimethylxanthine (caffeine) level)	3.000000e-09
GCST003848_1	Caffeine metabolism (plasma 1,3-dimethylxanthine (theophylline) level)	1.000000e-07
GCST003848_2	Caffeine metabolism (plasma 1,3-dimethylxanthine (theophylline) level)	1.000000e-08
GCST003848_3	Caffeine metabolism (plasma 1,3-dimethylxanthine (theophylline) level)	2.000000e-07
GCST003848_4	Caffeine metabolism (plasma 1,3-dimethylxanthine (theophylline) level)	1.000000e-07
GCST003851_4	Caffeine metabolism (plasma 1,7-dimethylxanthine (paraxanthine) to 1,3,7-trimethylxanthine (caffeine) ratio)	3.000000e-07
GCST003851_5	Caffeine metabolism (plasma 1,7-dimethylxanthine (paraxanthine) to 1,3,7-trimethylxanthine (caffeine) ratio)	3.000000e-14
GCST003851_6	Caffeine metabolism (plasma 1,7-dimethylxanthine (paraxanthine) to 1,3,7-trimethylxanthine (caffeine) ratio)	3.000000e-11
GCST003851_7	Caffeine metabolism (plasma 1,7-dimethylxanthine (paraxanthine) to 1,3,7-trimethylxanthine (caffeine) ratio)	4.000000e-15
GCST003851_8	Caffeine metabolism (plasma 1,7-dimethylxanthine (paraxanthine) to 1,3,7-trimethylxanthine (caffeine) ratio)	9.000000e-22
GCST004412_7	Craniofacial microsomia	1.000000e-23
GCST010108_21	Coffee consumption (cups per day)	2.000000e-08
GCST90002395_177	Mean platelet volume	4.000000e-15

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004330	coffee consumption
EFO:0007872	caffeine metabolite measurement
EFO:0006782	cups of coffee per day measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Tetrachlorodibenzodioxin	affects cotreatment, increases expression	3
Estradiol	affects cotreatment, increases expression	2
Tobacco Smoke Pollution	increases expression	2
Cadmium Chloride	decreases expression, increases abundance, increases expression	2
FR900359	affects phosphorylation	1
bisphenol F	affects cotreatment, increases expression	1
chloroacetaldehyde	increases expression	1
triphenyl phosphate	affects expression	1
beta-lapachone	increases expression	1
sodium arsenite	increases expression	1
coumarin	decreases phosphorylation	1
di-n-butylphosphoric acid	affects expression	1
abrine	increases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases expression	1
3-(2-hydroxy-4-(2-methylnonan-2-yl)phenyl)cyclohexan-1-ol	decreases expression	1
Air Pollutants	affects expression, increases abundance	1
Benzo(a)pyrene	increases expression	1
Cadmium	increases abundance, increases expression	1
Caffeine	decreases phosphorylation	1
Dexamethasone	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Hydrogen Peroxide	affects expression	1
Indomethacin	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1
Oxygen	affects expression	1
Ozone	affects expression, increases abundance	1
Quercetin	increases expression	1
Smoke	decreases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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