GDE1

Summary

GDE1 (glycerophosphodiester phosphodiesterase 1, HGNC:29644) is a protein-coding gene on chromosome 16p12.3, encoding Glycerophosphodiester phosphodiesterase 1 (Q9NZC3). Hydrolyzes the phosphodiester bond of glycerophosphodiesters such as glycerophosphoinositol (GroPIns) and glycerophosphoethanolamine (GroPEth), to yield a glycerol phosphate and an alcohol.

Predicted to enable glycerophosphodiester phosphodiesterase activity; glycerophosphoinositol glycerophosphodiesterase activity; and lysophospholipase activity. Predicted to be involved in N-acylethanolamine metabolic process; ethanolamine metabolic process; and phospholipid metabolic process. Predicted to be located in membrane. Predicted to be active in plasma membrane.

Source: NCBI Gene 51573 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 51 total
• MANE Select transcript: NM_016641

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29644
Approved symbol	GDE1
Name	glycerophosphodiester phosphodiesterase 1
Location	16p12.3
Locus type	gene with protein product
Status	Approved
Aliases	MIR16
Ensembl gene	ENSG00000006007
Ensembl biotype	protein_coding
OMIM	605943
Entrez	51573

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 4 protein_coding, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000353258, ENST00000563645, ENST00000564172, ENST00000569773, ENST00000569899, ENST00000858770

RefSeq mRNA: 3 — MANE Select: NM_016641 NM_001324066, NM_001324067, NM_016641

CCDS: CCDS10578

Canonical transcript exons

ENST00000353258 — 6 exons

Exon	Start	End
ENSE00000829404	19517014	19517189
ENSE00001223808	19501693	19503617
ENSE00002610808	19521704	19522098
ENSE00003468668	19507687	19507779
ENSE00003540866	19504881	19505092
ENSE00003589903	19510839	19510944

Expression profiles

Bgee: expression breadth ubiquitous, 285 present calls, max score 97.11.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 43.3016 / max 308.7960, expressed in 1822 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
156574	31.1571	1819
156572	6.3609	1753
156573	5.7836	1731

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left ventricle myocardium	UBERON:0006566	97.11	gold quality
cardiac muscle of right atrium	UBERON:0003379	97.06	gold quality
rectum	UBERON:0001052	96.89	gold quality
myocardium	UBERON:0002349	96.64	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	96.62	gold quality
heart right ventricle	UBERON:0002080	96.31	gold quality
islet of Langerhans	UBERON:0000006	96.30	gold quality
prefrontal cortex	UBERON:0000451	96.24	gold quality
stromal cell of endometrium	CL:0002255	96.20	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	96.07	gold quality
biceps brachii	UBERON:0001507	95.91	gold quality
nasal cavity mucosa	UBERON:0001826	95.86	gold quality
colonic mucosa	UBERON:0000317	95.78	gold quality
mucosa of sigmoid colon	UBERON:0004993	95.48	gold quality
sigmoid colon	UBERON:0001159	95.36	gold quality
monocyte	CL:0000576	95.35	gold quality
muscle layer of sigmoid colon	UBERON:0035805	95.34	gold quality
lower esophagus muscularis layer	UBERON:0035833	95.25	gold quality
lower esophagus	UBERON:0013473	95.24	gold quality
diaphragm	UBERON:0001103	95.05	gold quality
mucosa of transverse colon	UBERON:0004991	95.04	gold quality
amygdala	UBERON:0001876	95.02	gold quality
mononuclear cell	CL:0000842	94.95	gold quality
large intestine	UBERON:0000059	94.95	gold quality
colon	UBERON:0001155	94.95	gold quality
putamen	UBERON:0001874	94.94	gold quality
transverse colon	UBERON:0001157	94.86	gold quality
cardiac ventricle	UBERON:0002082	94.84	gold quality
cardiac atrium	UBERON:0002081	94.83	gold quality
heart left ventricle	UBERON:0002084	94.82	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	20.20

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

78 targeting GDE1, 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-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-3162-3P	100.00	65.37	363
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-8087	99.90	69.55	1351
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-659-3P	99.85	70.69	1620
HSA-MIR-139-5P	99.80	69.50	1399
HSA-MIR-378G	99.71	64.90	1106
HSA-MIR-3059-5P	99.70	69.93	2491
HSA-MIR-3618	99.69	68.57	1012
HSA-MIR-586	99.65	70.40	2051
HSA-MIR-4666B	99.64	68.69	1282
HSA-MIR-488-3P	99.61	68.79	1731
HSA-MIR-497-3P	99.61	69.71	1990
HSA-MIR-12122	99.56	69.33	1672
HSA-MIR-4437	99.52	65.29	1266
HSA-MIR-409-3P	99.50	66.33	1192
HSA-MIR-140-5P	99.44	67.20	792
HSA-MIR-520E-5P	99.27	68.90	1513

Literature-anchored findings (GeneRIF, showing 22)

• regulation by by stimulation of G protein-coupled receptors (PMID:12576545)
• Glycerophosphodiesterase has robust activity on glycerophospho-N-acyl ethanolamines (GP-NAEs) which are precursors for the N-acyl ethanolamines including the endocannabinoid anandamide. Thus, GDE1 may participate in anandamide biosynthesis. (PMID:18227059)
• These findings suggest that genes other than miR-15a and miR-16 may explain the prognostic significance of 13q14 deletions in patients with multiple myeloma (PMID:20031211)
• Results suggest an important role of miR-16 in the regulation of Wip1 phosphatase in the DNA damage response and mammary tumorigenesis. (PMID:20668064)
• miR-16 and miR-21 are directly regulated by the transcription factor NF-kappaB and yet nicotine-promoted cell proliferation is mediated via EP2/4 receptors. (PMID:21081469)
• This study demonistrated that miR-15a and 16-1 are downregulated in CD4+ T cells of multiple sclerosis relapsing patients. (PMID:22463747)
• Up-regulation of miR-16 is associated with triple negative breast cancer. (PMID:23405235)
• miR-16 and miR-26a target checkpoint kinases Wee1 and Chk1 in response to p53 activation by genotoxic stress. (PMID:24336073)
• YAP1 was confirmed to be a functional target of miR-15a and miR-16-1 in GAC. (PMID:25743273)
• Our data indicate differential concentrations of plasma miR-16, miR-107, miR-130a and miR-146a in different breast cancer subtypes, suggesting a potential role of these miRs in breast cancer biology and tumor progression. (PMID:26033453)
• Quercetin decreases claudin-2 expression mediated by up-regulation of miR-16 expression and instability of claudin-2 mRNA in lung adenocarcinoma cells. (PMID:26061016)
• The expression levels of two target genes, Myb and VEGFR2, were affected significantly by miR-16, while glucose administration inhibited miR-16 expression and enhanced tumor cell proliferation and migration. (PMID:26934556)
• we identified cyclin J and far upstream element-binding protein 1 (FUBP1) as novel miR-16 targets, which mediate miR-16 antiproliferative effects. (PMID:27157613)
• miR-15a/16 may function as a tumor suppressor in MM through multiple regulatory mechanisms (PMID:27596960)
• Our outcomes suggest that miR-15a/16 maintain the retinal endothelial cell barrier by reducing TGFbeta3/VEGF signaling and increasing levels of key tight junction proteins. (PMID:28774775)
• The mRNA of TYRP1 is now found to sequester the tumour suppressor miR-16. (PMID:29087386)
• this study shows that HTR$ gene expression regulation is affected by mir-16 and mir-103 single nucleotide polymorphisms (PMID:29089619)
• Sera samples from inflammatory bowel disease (IBD) patients showed higher level of miR-16, miR-21, and miR-223, but not miR-155, compared to controls and was higher in Crohn’s disease (CD) than in ulcerative colitis (UC) patients. (PMID:29668922)
• MiR15a/16 inhibited the components of TGF-beta signaling pathways. (PMID:29803177)
• Long Noncoding RNA DLX6-AS1 Promotes the Progression in Cervical Cancer by Targeting miR-16-5p/ARPP19 Axis. (PMID:32077747)
• Solanine inhibits proliferation and promotes apoptosis of the human leukemia cells by targeting the miR-16/Bcl-2 axis. (PMID:32862612)
• Downregulation of exosomal let-7d and miR-16 in idiopathic pulmonary fibrosis. (PMID:34088304)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	gde1	ENSDARG00000055108
mus_musculus	Gde1	ENSMUSG00000033917
rattus_norvegicus	Gde1	ENSRNOG00000050445
caenorhabditis_elegans		WBGENE00011929
caenorhabditis_elegans		WBGENE00022532

Paralogs (5): GDPD3 (ENSG00000102886), GDPD2 (ENSG00000130055), GDPD1 (ENSG00000153982), GDPD5 (ENSG00000158555), GDPD4 (ENSG00000178795)

Protein

Protein identifiers

Glycerophosphodiester phosphodiesterase 1 — Q9NZC3 (reviewed: Q9NZC3)

Alternative names: Glycerophosphoinositol glycerophosphodiesterase GDE1, Lysophospholipase D GDE1, Membrane-interacting protein of RGS16, RGS16-interacting membrane protein

All UniProt accessions (4): Q9NZC3, H3BNA5, H3BRL5, H3BU22

UniProt curated annotations — full annotation on UniProt →

Function. Hydrolyzes the phosphodiester bond of glycerophosphodiesters such as glycerophosphoinositol (GroPIns) and glycerophosphoethanolamine (GroPEth), to yield a glycerol phosphate and an alcohol. Hydrolyzes glycerophospho-N-acylethanolamines to N-acylethanolamines in the brain and participates in bioactive N-acylethanolamine biosynthesis such as anandamide (an endocannabinoid), N-palmitoylethanolamine (an anti-inflammatory), and N-oleoylethanolamine (an anorexic). In addition, has a lysophospholipase D activity by hydrolyzing N-acyl-lysoplasmenylethanolamine (N-acyl-lysoPlsEt) to N-acylethanolamine. However lysophospholipase D activity is lower than glycerophosphodiester phosphodiesterase activity. Has little or no activity towards glycerophosphocholine.

Subunit / interactions. Interacts with PRAF2. Interacts with RGS16.

Subcellular location. Cell membrane. Cytoplasmic vesicle membrane.

Tissue specificity. Widely expressed.

Post-translational modifications. N-glycosylated.

Activity regulation. Inhibited by EDTA, calcium chloride, and zinc chloride. Enhanced by magnesium chloride. Glycerophosphodiester phosphodiesterase activity can be modulated by G-protein signaling pathways.

Similarity. Belongs to the glycerophosphoryl diester phosphodiesterase family.

RefSeq proteins (3): NP_001310995, NP_001310996, NP_057725* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR017946	PLC-like_Pdiesterase_TIM-brl	Homologous_superfamily
IPR030395	GP_PDE_dom	Domain

Pfam: PF03009

Enzyme classification (BRENDA):

• EC 3.1.4.44 — glycerophosphoinositol glycerophosphodiesterase (BRENDA: 4 organisms, 10 substrates, 10 inhibitors, 2 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

1 substrates with measured Km, best-characterized 1. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
1-(SN-GLYCERO-3-PHOSPHO)-1D-MYO-INOSITOL	12	1

Catalyzed reactions (Rhea), 9 shown:

• sn-glycero-3-phospho-1D-myo-inositol + H2O = myo-inositol + sn-glycerol 3-phosphate + H(+) (RHEA:16501)
• N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phosphoethanolamine + H2O = N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-ethanolamine + sn-glycerol 3-phosphate + H(+) (RHEA:45428)
• N-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine + H2O = N-(9Z-octadecenoyl) ethanolamine + sn-glycerol 3-phosphate + H(+) (RHEA:45432)
• N-hexadecanoyl-sn-glycero-3-phosphoethanolamine + H2O = N-hexadecanoylethanolamine + sn-glycerol 3-phosphate + H(+) (RHEA:45436)
• N-eicosanoyl-sn-glycero-3-phosphoethanolamine + H2O = N-eicosanoyl ethanolamine + sn-glycerol 3-phosphate + H(+) (RHEA:45440)
• N-(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-sn-glycero-3-phosphoethanolamine + H2O = N-(4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl ethanolamine + sn-glycerol 3-phosphate + H(+) (RHEA:45444)
• 1-O-(1Z-octadecenyl)-sn-glycero-3-phospho-N-hexadecanoyl-ethanolamine + H2O = 1-O-(1Z-octadecenyl)-sn-glycero-3-phosphate + N-hexadecanoylethanolamine + H(+) (RHEA:53184)
• 1-O-(1Z-octadecenyl)-sn-glycero-3-phospho-(N-9Z-octadecenoyl)-ethanolamine + H2O = 1-O-(1Z-octadecenyl)-sn-glycero-3-phosphate + N-(9Z-octadecenoyl) ethanolamine + H(+) (RHEA:53188)
• 1-O-(1Z-octadecenyl)-sn-glycero-3-phospho-(N-5Z,8Z,11Z,14Z-eicosatetraenoyl)-ethanolamine + H2O = 1-O-(1Z-octadecenyl)-sn-glycero-3-phosphate + N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-ethanolamine + H(+) (RHEA:53192)

UniProt features (14 total): topological domain 3, binding site 3, glycosylation site 2, sequence variant 2, transmembrane region 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NZC3-F1	94.29	0.92

Functional residue map

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

Ligand- & substrate-binding residues (3): 97; 99; 174

Glycosylation sites (2): 168, 198

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-6814848	Glycerophospholipid catabolism

MSigDB gene sets: 185 (showing top): GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, KAAB_FAILED_HEART_ATRIUM_DN, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, MORF_SKP1A, GOBP_ORGANOPHOSPHATE_CATABOLIC_PROCESS, GOBP_GLYCEROPHOSPHOLIPID_METABOLIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS, GOBP_GLYCEROPHOSPHOLIPID_CATABOLIC_PROCESS, GOBP_GLYCEROLIPID_CATABOLIC_PROCESS, GOBP_LIPID_CATABOLIC_PROCESS, GOBP_PHOSPHOLIPID_CATABOLIC_PROCESS, DANG_BOUND_BY_MYC

GO Biological Process (5): ethanolamine metabolic process (GO:0006580), lipid metabolic process (GO:0006629), phospholipid metabolic process (GO:0006644), glycerophospholipid catabolic process (GO:0046475), N-acylethanolamine metabolic process (GO:0070291)

GO Molecular Function (7): phosphatidylcholine lysophospholipase A1 activity (GO:0004622), glycerophosphodiester phosphodiesterase activity (GO:0008889), metal ion binding (GO:0046872), glycerophosphoinositol glycerophosphodiesterase activity (GO:0047395), protein binding (GO:0005515), phosphoric diester hydrolase activity (GO:0008081), hydrolase activity (GO:0016787)

GO Cellular Component (4): plasma membrane (GO:0005886), membrane (GO:0016020), cytoplasmic vesicle membrane (GO:0030659), cytoplasmic vesicle (GO:0031410)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
PI Metabolism	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
primary alcohol metabolic process	2
phosphoric diester hydrolase activity	2
amine metabolic process	1
primary metabolic process	1
lipid metabolic process	1
organophosphate metabolic process	1
glycerophospholipid metabolic process	1
phospholipid catabolic process	1
glycerolipid catabolic process	1
lysophospholipase A1 activity	1
cation binding	1
binding	1
phosphoric ester hydrolase activity	1
catalytic activity	1
membrane	1
cell periphery	1
cellular anatomical structure	1
vesicle membrane	1
cytoplasmic vesicle	1
cytoplasm	1
intracellular vesicle	1

Protein interactions and networks

STRING

1036 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GDE1	RGS16	O15492	905
GDE1	ABHD4	Q8TB40	864
GDE1	NAPEPLD	Q6IQ20	854
GDE1	RGS2	P41220	690
GDE1	FAAH	O00519	674
GDE1	MGLL	Q99685	638
GDE1	DAGLA	Q9Y4D2	635
GDE1	DAGLB	Q8NCG7	634
GDE1	NAAA	Q02083	614
GDE1	ABHD12	Q8N2K0	610
GDE1	ABHD6	Q9BV23	608
GDE1	PTPN22	Q9Y2R2	555
GDE1	FAAH2	Q6GMR7	551
GDE1	GPCPD1	Q9NPB8	536
GDE1	GPR55	Q9Y2T6	498

IntAct

26 interactions, top by confidence:

A	B	Type	Score
CXorf58	GDE1	psi-mi:“MI:0915”(physical association)	0.560
SLC10A1	GDE1	psi-mi:“MI:0915”(physical association)	0.560
GDE1	GAPDHS	psi-mi:“MI:0914”(association)	0.530
REEP5	SCAMP1	psi-mi:“MI:0914”(association)	0.530
REEP5	PLSCR1	psi-mi:“MI:0914”(association)	0.530
GDE1	ADRA1A	psi-mi:“MI:0915”(physical association)	0.370
CLGN	GDE1	psi-mi:“MI:0915”(physical association)	0.370
Npc1	ESYT2	psi-mi:“MI:0914”(association)	0.350
APOA2	TMEM131L	psi-mi:“MI:0914”(association)	0.350
CYB5B	QSOX1	psi-mi:“MI:0914”(association)	0.350
RNF126	GET3	psi-mi:“MI:0914”(association)	0.350
CXorf58	TGFBR2	psi-mi:“MI:0914”(association)	0.350
ADCY2	ANKMY2	psi-mi:“MI:0914”(association)	0.350
REEP5	ESYT2	psi-mi:“MI:0914”(association)	0.350
GDE1	UBAC2	psi-mi:“MI:0914”(association)	0.350
SLC22A24	ADCY3	psi-mi:“MI:0914”(association)	0.350
SLC35A5	CLGN	psi-mi:“MI:0914”(association)	0.350
SLC7A6	FAAH	psi-mi:“MI:0914”(association)	0.350
GDE1	SLC10A1	psi-mi:“MI:0915”(physical association)	0.000
GDE1	cpfC2	psi-mi:“MI:0915”(physical association)	0.000
ftsB	GDE1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (61): ATAD3C (Affinity Capture-MS), SLC4A7 (Affinity Capture-MS), REEP5 (Affinity Capture-MS), FAM84B (Affinity Capture-MS), GAPDHS (Affinity Capture-MS), PLSCR1 (Affinity Capture-MS), ATL3 (Affinity Capture-MS), TMEM109 (Affinity Capture-MS), PROCR (Affinity Capture-MS), BRI3BP (Affinity Capture-MS), GDE1 (Affinity Capture-MS), GDE1 (Affinity Capture-MS), GDE1 (Affinity Capture-MS), SLC4A7 (Affinity Capture-MS), FAM84B (Affinity Capture-MS)

ESM2 similar proteins: A2A7Z8, A7LB60, P08910, P0DKC5, P0DKC6, P22760, P70683, P83006, Q05AK6, Q0P5B7, Q13093, Q14032, Q1LZ86, Q28017, Q32LS6, Q4R2Y9, Q4V8A1, Q502J0, Q5EA42, Q5PPS7, Q5VUY0, Q5VUY2, Q5XI64, Q5ZJL8, Q5ZKL5, Q60963, Q63276, Q6DHN0, Q6GLL2, Q6IE26, Q6P093, Q7L211, Q7M370, Q7SY73, Q7Z5M8, Q802V6, Q80UX8, Q8BM81, Q8IUS5, Q8R2Y0

Diamond homologs: A0A8F4N283, O07592, O30405, P09394, P37965, P47535, P54527, P75367, P9WLF0, P9WLF1, Q06282, Q08959, Q3T0T0, Q3TT99, Q640M6, Q6W3E5, Q7L5L3, Q8RB32, Q95JR7, Q99LY2, Q9C907, Q9ESM6, Q9HCC8, Q9JL56, Q9NZC3, Q9SD81, P10908, P55427, P75212, Q0VGK4, Q10003, Q8N9F7, Q9CRY7, Q9JL55, O14169, P9WMU2, P9WMU3, Q3KTM2, Q8WTR4, P47625

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	40
Likely benign	0
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

520 predictions. Top by Δscore:

Variant	Effect	Δscore
16:19510833:CTGTA:C	donor_loss	1.0000
16:19510834:TGTAC:T	donor_loss	1.0000
16:19510835:GTACC:G	donor_loss	1.0000
16:19510836:TACCT:T	donor_loss	1.0000
16:19510838:C:CT	donor_loss	1.0000
16:19510940:CATTC:C	acceptor_gain	1.0000
16:19510941:ATTC:A	acceptor_gain	1.0000
16:19510942:TTC:T	acceptor_gain	1.0000
16:19510943:TC:T	acceptor_gain	1.0000
16:19510944:CCTG:C	acceptor_gain	1.0000
16:19510945:C:CC	acceptor_gain	1.0000
16:19510946:T:C	acceptor_loss	1.0000
16:19517009:CTTA:C	donor_loss	1.0000
16:19517010:TTA:T	donor_loss	1.0000
16:19517011:TA:T	donor_loss	1.0000
16:19517012:A:AC	donor_gain	1.0000
16:19517012:A:AT	donor_loss	1.0000
16:19517013:C:CA	donor_gain	1.0000
16:19517013:CCTGA:C	donor_gain	1.0000
16:19517191:T:C	acceptor_gain	1.0000
16:19517191:T:TC	acceptor_gain	1.0000
16:19521698:TCTCA:T	donor_loss	1.0000
16:19521699:CTCAC:C	donor_loss	1.0000
16:19521700:TCA:T	donor_loss	1.0000
16:19521701:CAC:C	donor_loss	1.0000
16:19521702:ACC:A	donor_loss	1.0000
16:19521703:C:A	donor_loss	1.0000
16:19504879:A:AC	donor_gain	0.9900
16:19504880:C:CC	donor_gain	0.9900
16:19504931:C:CT	donor_gain	0.9900

AlphaMissense

2204 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:19521753:C:G	R71P	0.997
16:19504969:C:G	D254H	0.996
16:19507718:A:T	V202D	0.996
16:19507723:A:C	S200R	0.996
16:19507723:A:T	S200R	0.996
16:19507725:T:G	S200R	0.996
16:19503601:A:G	W289R	0.995
16:19503601:A:T	W289R	0.995
16:19503571:A:G	W299R	0.994
16:19503571:A:T	W299R	0.994
16:19510855:T:A	K176I	0.994
16:19521725:G:C	N80K	0.994
16:19521725:G:T	N80K	0.994
16:19505061:G:T	A223E	0.993
16:19505062:C:G	A223P	0.993
16:19504968:T:A	D254V	0.992
16:19517125:A:T	V109D	0.992
16:19521754:G:T	R71S	0.992
16:19504968:T:G	D254A	0.991
16:19507708:G:C	F205L	0.991
16:19507708:G:T	F205L	0.991
16:19507710:A:G	F205L	0.991
16:19510854:T:A	K176N	0.991
16:19510854:T:G	K176N	0.991
16:19510904:C:G	A160P	0.991
16:19521732:G:T	P78H	0.991
16:19521736:C:G	A77P	0.991
16:19521715:C:G	A84P	0.989
16:19521750:C:T	G72D	0.989
16:19504920:C:A	G270V	0.988

dbSNP variants (sampled 300 via entrez): RS1000258770 (16:19520813 A>T), RS1000339648 (16:19501461 A>C), RS1000391769 (16:19513568 A>C,G), RS1000417210 (16:19505686 C>T), RS1000520740 (16:19522057 G>A,C,T), RS1000696908 (16:19514887 C>T), RS1000761388 (16:19513292 T>C), RS1000920389 (16:19506324 C>CA), RS1001069310 (16:19513372 T>A,C,G), RS1001084459 (16:19520699 T>A,C), RS1001135609 (16:19515187 G>C), RS1001318747 (16:19513697 A>G), RS1001585269 (16:19509405 G>C), RS1001641001 (16:19519959 T>A), RS1001711485 (16:19520198 A>C)

Disease associations

OMIM: gene MIM:605943 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST009391_486	Metabolite levels	7.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010389	phosphatidylcholine 40:6 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	5
triphenyl phosphate	affects expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
bisphenol A	increases methylation, affects cotreatment	1
trichostatin A	affects expression	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
corosolic acid	increases expression	1
(+)-JQ1 compound	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Arsenic Trioxide	decreases response to substance	1
Fulvestrant	affects cotreatment, increases methylation	1
Acrolein	increases abundance, affects cotreatment, increases oxidation	1
Air Pollutants	increases oxidation, affects cotreatment, increases abundance	1
Cisplatin	increases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Ozone	affects cotreatment, increases oxidation, increases abundance	1
Thiram	decreases expression	1
Urethane	increases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Cyclosporine	decreases expression	1
Okadaic Acid	increases expression	1
Copper Sulfate	decreases expression	1
Lactic Acid	decreases expression	1
Volatile Organic Compounds	affects cotreatment, increases oxidation	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_B1SS	Abcam HeLa GDE1 KO	Cancer cell line	Female

Clinical trials (associated diseases)

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