GDPD5

Summary

GDPD5 (glycerophosphodiester phosphodiesterase domain containing 5, HGNC:28804) is a protein-coding gene on chromosome 11q13.4-q13.5, encoding Glycerophosphodiester phosphodiesterase domain-containing protein 5 (Q8WTR4). Glycerophosphodiester phosphodiesterase that promotes neurite formation and drives spinal motor neuron differentiation.

Predicted to enable glycerophosphodiester phosphodiesterase activity. Predicted to be involved in positive regulation of cell cycle and positive regulation of neuron differentiation. Predicted to act upstream of or within negative regulation of Notch signaling pathway; neuron differentiation; and regulation of timing of cell differentiation. Predicted to be located in axon; neuronal cell body; and perinuclear endoplasmic reticulum. Predicted to be active in plasma membrane.

Source: NCBI Gene 81544 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 112 total
• MANE Select transcript: NM_030792

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28804
Approved symbol	GDPD5
Name	glycerophosphodiester phosphodiesterase domain containing 5
Location	11q13.4-q13.5
Locus type	gene with protein product
Status	Approved
Aliases	PP1665, GDE2
Ensembl gene	ENSG00000158555
Ensembl biotype	protein_coding
OMIM	609632
Entrez	81544

Gene structure

Transcript identifiers

Ensembl transcripts: 34 — 25 protein_coding, 5 protein_coding_CDS_not_defined, 3 retained_intron, 1 nonsense_mediated_decay

ENST00000336898, ENST00000443276, ENST00000524785, ENST00000526177, ENST00000527322, ENST00000527820, ENST00000528031, ENST00000529095, ENST00000529721, ENST00000531441, ENST00000531561, ENST00000531759, ENST00000532435, ENST00000533784, ENST00000533805, ENST00000533911, ENST00000534322, ENST00000887012, ENST00000887013, ENST00000887014, ENST00000887015, ENST00000887016, ENST00000887017, ENST00000887018, ENST00000887019, ENST00000926863, ENST00000926864, ENST00000926865, ENST00000926866, ENST00000926867, ENST00000953508, ENST00000953509, ENST00000953510, ENST00000953511

RefSeq mRNA: 3 — MANE Select: NM_030792 NM_001351167, NM_001351168, NM_030792

CCDS: CCDS8238, CCDS86229, CCDS86230

Canonical transcript exons

ENST00000336898 — 17 exons

Exon	Start	End
ENSE00001351126	75490237	75490320
ENSE00002170887	75525210	75525941
ENSE00003460329	75443136	75443286
ENSE00003463718	75448977	75449122
ENSE00003467874	75456757	75456816
ENSE00003486577	75457693	75457786
ENSE00003511237	75477619	75477795
ENSE00003515973	75449517	75449610
ENSE00003517183	75444413	75444495
ENSE00003528535	75449885	75449983
ENSE00003533546	75441646	75441803
ENSE00003545432	75441163	75441310
ENSE00003552465	75434640	75435655
ENSE00003589091	75442363	75442581
ENSE00003626459	75436936	75437048
ENSE00003685839	75439879	75439961
ENSE00003787906	75462786	75462889

Expression profiles

Bgee: expression breadth ubiquitous, 264 present calls, max score 96.77.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 3.1602 / max 88.2397, expressed in 1260 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
121363	1.9394	943
121364	0.9860	560
121361	0.1942	91
121360	0.0406	15

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
spleen	UBERON:0002106	96.77	gold quality
right hemisphere of cerebellum	UBERON:0014890	95.57	gold quality
cerebellar hemisphere	UBERON:0002245	95.09	gold quality
cerebellar cortex	UBERON:0002129	95.00	gold quality
granulocyte	CL:0000094	94.94	gold quality
cortical plate	UBERON:0005343	93.70	gold quality
cerebellum	UBERON:0002037	93.51	gold quality
right testis	UBERON:0004534	93.47	gold quality
parotid gland	UBERON:0001831	93.36	gold quality
left testis	UBERON:0004533	92.98	gold quality
tibial nerve	UBERON:0001323	92.82	gold quality
body of pancreas	UBERON:0001150	91.94	gold quality
omental fat pad	UBERON:0010414	91.18	gold quality
adipose tissue of abdominal region	UBERON:0007808	91.14	gold quality
peritoneum	UBERON:0002358	91.12	gold quality
adipose tissue	UBERON:0001013	90.88	gold quality
subcutaneous adipose tissue	UBERON:0002190	90.54	gold quality
testis	UBERON:0000473	90.41	gold quality
placenta	UBERON:0001987	90.20	gold quality
sperm	CL:0000019	90.08	gold quality
connective tissue	UBERON:0002384	89.98	gold quality
male germ cell	CL:0000015	89.91	gold quality
lateral nuclear group of thalamus	UBERON:0002736	89.66	gold quality
sural nerve	UBERON:0015488	89.20	gold quality
pigmented layer of retina	UBERON:0001782	88.83	gold quality
body of uterus	UBERON:0009853	88.39	gold quality
saliva-secreting gland	UBERON:0001044	87.83	gold quality
minor salivary gland	UBERON:0001830	87.37	gold quality
pituitary gland	UBERON:0000007	86.81	gold quality
ascending aorta	UBERON:0001496	86.06	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.92

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

31 targeting GDPD5, 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-6798-5P	100.00	65.77	699
HSA-MIR-4713-3P	100.00	65.92	505
HSA-MIR-4650-5P	99.98	64.69	999
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-766-3P	99.47	65.24	1811
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-544B	99.18	67.41	1632
HSA-MIR-485-5P	99.10	64.78	1889
HSA-MIR-6884-5P	99.10	64.50	1987
HSA-MIR-1909-3P	99.03	66.56	1662
HSA-MIR-622	98.99	66.48	1050
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-5001-3P	98.91	67.28	1394
HSA-MIR-4317	98.49	67.09	987
HSA-MIR-4252	98.45	66.37	987
HSA-MIR-660-3P	98.14	66.04	1434
HSA-MIR-6742-3P	97.95	64.50	1490
HSA-MIR-4294	97.86	65.72	1110
HSA-MIR-1289	97.46	65.37	655
HSA-MIR-3187-3P	97.38	65.80	904
HSA-MIR-873-3P	96.84	66.09	786
HSA-MIR-1292-5P	96.74	62.14	238
HSA-MIR-4701-5P	96.45	68.41	1121
HSA-MIR-588	96.45	68.36	1127
HSA-MIR-7108-5P	96.42	66.17	598
HSA-MIR-4471	95.11	66.84	755

Literature-anchored findings (GeneRIF, showing 9)

• GDPD5 was widely expressed in human tissues and the expression levels in kidney and prostate were relatively low (PMID:17578682)
• Identification of GDPD5 as a glycerophosphocholine phosphodiesterase that probably participates in the regulation of choline phospholipid metabolism in breast cancer. (PMID:22279038)
• GDPD5 expression is strongly associated with favorable outcome in neuroblastoma. GDE2 induces differentiation of neuroblastoma cells, suppresses cell motility, and opposes RhoA-driven neurite retraction. (PMID:27693046)
• Data suggest that GDE2/gdpd5 play roles in pancreatic organogenesis; gdpd5 knockdown leads to defects in differentiation of pancreas in zebrafish embryos; studies with recombinant fusion proteins suggest similar roles for homologous human GDE2 and zebrafish gdpd5. (PMID:29203233)
• miR-195-5p is a potent suppressor of GDPD5 and that, as such, it significantly increases chemosensitivity and apoptosis in chemoresistant colorectal cells. (PMID:29635904)
• GDE2-RECK controls ADAM10 alpha-secretase-mediated cleavage of amyloid precursor protein. (PMID:33731436)
• Circ_0007142 downregulates miR-874-3p-mediated GDPD5 on colorectal cancer cells. (PMID:33797091)
• Loss of GDE2 leads to complex behavioral changes including memory impairment. (PMID:38575965)
• The Six-Transmembrane Enzyme GDE2 Is Required for the Release of Molecularly Distinct Small Extracellular Vesicles from Neurons. (PMID:39272985)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	gdpd5b	ENSDARG00000076962
danio_rerio	gdpd5a	ENSDARG00000077284
mus_musculus	Gdpd5	ENSMUSG00000035314
rattus_norvegicus	Gdpd5	ENSRNOG00000036859

Paralogs (5): GDE1 (ENSG00000006007), GDPD3 (ENSG00000102886), GDPD2 (ENSG00000130055), GDPD1 (ENSG00000153982), GDPD4 (ENSG00000178795)

Protein

Protein identifiers

Glycerophosphodiester phosphodiesterase domain-containing protein 5 — Q8WTR4 (reviewed: Q8WTR4)

Alternative names: Glycerophosphocholine phosphodiesterase GDPD5, Glycerophosphodiester phosphodiesterase 2, Phosphoinositide phospholipase C GDPD5

All UniProt accessions (4): E9PJU5, Q8WTR4, H0YEF5, Q8NDN3

UniProt curated annotations — full annotation on UniProt →

Function. Glycerophosphodiester phosphodiesterase that promotes neurite formation and drives spinal motor neuron differentiation. Mediates the cleavage of glycosylphosphatidylinositol (GPI) anchor of target proteins: removes the GPI-anchor of RECK, leading to release RECK from the plasma membrane. May contribute to the osmotic regulation of cellular glycerophosphocholine.

Subunit / interactions. Interacts with PRDX1; forms a mixed-disulfide with PRDX1, leading to disrupt intramolecular disulfide bond between Cys-25 and Cys-571.

Subcellular location. Endomembrane system. Cytoplasm. Perinuclear region. Cell projection. Growth cone.

Post-translational modifications. Intramolecular disulfide bond between Cys-25 and Cys-571 is reduced by PRDX1.

Similarity. Belongs to the glycerophosphoryl diester phosphodiesterase family.

Isoforms (5)

UniProt ID	Names	Canonical?
Q8WTR4-1	1	yes
Q8WTR4-2	2
Q8WTR4-3	3
Q8WTR4-4	4
Q8WTR4-5	5

RefSeq proteins (3): NP_001338096, NP_001338097, NP_110419* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF03009, PF13653

Enzyme classification (BRENDA):

• EC 3.1.4.11 — phosphoinositide phospholipase C (BRENDA: 69 organisms, 175 substrates, 159 inhibitors, 27 Km, 0 kcat entries)
• EC 3.1.4.2 — glycerophosphocholine phosphodiesterase (BRENDA: 27 organisms, 58 substrates, 52 inhibitors, 35 Km, 18 kcat entries)
• EC 3.1.4.46 — glycerophosphodiester phosphodiesterase (BRENDA: 38 organisms, 62 substrates, 23 inhibitors, 29 Km, 19 kcat entries)

Substrate kinetics (BRENDA)

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

Substrate	Km (mM)	Measurements
1-PHOSPHATIDYL-1D-MYO-INOSITOL 4,5-BISPHOSPHATE	0.006–0.45	8
PHOSPHATIDYLINOSITOL	0.012–100	7
1-PHOSPHATIDYL-1D-MYO-INOSITOL	0.058–18.7	6
BIS(P-NITROPHENYL) PHOSPHATE	0.12–3.95	5
GLYCEROPHOSPHOCHOLINE	0.036–2	5
P-NITROPHENYL PHOSPHATE	0.12–49	5
GLYCEROPHOSPHOCHOLINE	0.23–0.65	4
SN-GLYCERO 3-PHOSPHOCHOLINE	0.6–5.7	4
PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE	0.031–0.182	3
GLYCEROPHOSPHOETHANOLAMINE	0.2–0.22	3
GLYCEROPHOSPHOGLYCEROL	0.2–0.62	3
GLYCEROPHOSPHOETHANOLAMINE	0.24–1.2	2
SN-GLYCERO 3-PHOSPHORYLCHOLINE	0.31–1.2	2
BIS(P-NITROPHENYL PHOSPHATE)	3.5–7	2
GLYCEROPHOSPHOINOSITOL	0.39	2

Catalyzed reactions (Rhea), 2 shown:

• sn-glycerol 3-phosphocholine + H2O = sn-glycerol 3-phosphate + choline + H(+) (RHEA:16061)
• a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-4,5-bisphosphate) + H2O = 1D-myo-inositol 1,4,5-trisphosphate + a 1,2-diacyl-sn-glycerol + H(+) (RHEA:33179)

UniProt features (30 total): topological domain 7, transmembrane region 6, glycosylation site 5, splice variant 4, disulfide bond 2, sequence conflict 2, chain 1, domain 1, region of interest 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8WTR4-F1	86.36	0.72

Functional residue map

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

Disulfide bonds (2): 15–18, 25–571

Glycosylation sites (5): 301, 336, 352, 374, 448

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-6814848	Glycerophospholipid catabolism

MSigDB gene sets: 152 (showing top): CREL_01, GOBP_POSITIVE_REGULATION_OF_NEURON_DIFFERENTIATION, GOBP_NEUROGENESIS, chr11q13, CEBPB_01, NFKB_C, GOBP_REGULATION_OF_NEURON_DIFFERENTIATION, GOBP_POSITIVE_REGULATION_OF_CELL_DIFFERENTIATION, ENGELMANN_CANCER_PROGENITORS_UP, GGGNNTTTCC_NFKB_Q6_01, GOZGIT_ESR1_TARGETS_UP, GOBP_LIPID_METABOLIC_PROCESS, NIKOLSKY_BREAST_CANCER_11Q12_Q14_AMPLICON, GOCC_NEURON_PROJECTION, GOBP_POSITIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS

GO Biological Process (4): lipid metabolic process (GO:0006629), nervous system development (GO:0007399), positive regulation of neuron differentiation (GO:0045666), positive regulation of cell differentiation (GO:0045597)

GO Molecular Function (6): phosphatidylinositol-4,5-bisphosphate phospholipase C activity (GO:0004435), glycerophosphodiester phosphodiesterase activity (GO:0008889), glycerophosphocholine phosphodiesterase activity (GO:0047389), protein binding (GO:0005515), phosphoric diester hydrolase activity (GO:0008081), hydrolase activity (GO:0016787)

GO Cellular Component (7): plasma membrane (GO:0005886), endomembrane system (GO:0012505), growth cone (GO:0030426), perinuclear region of cytoplasm (GO:0048471), cytoplasm (GO:0005737), membrane (GO:0016020), cell projection (GO:0042995)

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
cellular anatomical structure	5
phosphoric diester hydrolase activity	2
primary metabolic process	1
system development	1
neuron differentiation	1
positive regulation of cell differentiation	1
regulation of neuron differentiation	1
cell differentiation	1
regulation of cell differentiation	1
positive regulation of cellular process	1
positive regulation of developmental process	1
C-type glycerophospholipase activity	1
binding	1
phosphoric ester hydrolase activity	1
catalytic activity	1
membrane	1
cell periphery	1
vacuole	1
plasma membrane	1
site of polarized growth	1
distal axon	1
cytoplasm	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

1040 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GDPD5	PRDX1	P35703	848
GDPD5	ISL2	Q96A47	762
GDPD5	SRXN1	Q9BYN0	719
GDPD5	MNX1	P50219	717
GDPD5	OLIG2	Q13516	616
GDPD5	GPCPD1	Q9NPB8	589
GDPD5	ISL1	P20663	587
GDPD5	PRDX2	P31945	498
GDPD5	CHKA	P35790	439
GDPD5	GPC6	Q9Y625	430
GDPD5	TBRG1	Q3YBR2	423
GDPD5	RECK	O95980	417
GDPD5	GDE1	Q9NZC3	409
GDPD5	ACER3	Q9NUN7	409
GDPD5	BNIPL	Q7Z465	408

IntAct

18 interactions, top by confidence:

A	B	Type	Score
CD27	TCAF2	psi-mi:“MI:0914”(association)	0.640
PEX5	GDPD5	psi-mi:“MI:0915”(physical association)	0.560
SIAH1	GDPD5	psi-mi:“MI:0915”(physical association)	0.560
GDPD5	PEX5	psi-mi:“MI:0915”(physical association)	0.560
GDPD5	SIAH1	psi-mi:“MI:0915”(physical association)	0.560
GDPD5	GOLIM4	psi-mi:“MI:0914”(association)	0.530
FDFT1	GDPD5	psi-mi:“MI:0915”(physical association)	0.400
GDPD5	KRTAP26-1	psi-mi:“MI:0915”(physical association)	0.370
P		psi-mi:“MI:0914”(association)	0.350
PRDM5	CASC3	psi-mi:“MI:0914”(association)	0.350
GDPD5	HSPA8	psi-mi:“MI:0914”(association)	0.350
GDPD5	TMEM120B	psi-mi:“MI:0914”(association)	0.350
IGSF8	HIP1R	psi-mi:“MI:0914”(association)	0.350
GDPD5	carB	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (82): GDPD5 (Two-hybrid), GDPD5 (Two-hybrid), GDPD5 (Two-hybrid), GDPD5 (Two-hybrid), KRTAP26-1 (Two-hybrid), GDPD5 (Affinity Capture-MS), ROBO1 (Affinity Capture-MS), GPD2 (Affinity Capture-MS), PIGQ (Affinity Capture-MS), SELT (Affinity Capture-MS), TMEM55A (Affinity Capture-MS), IGSF8 (Affinity Capture-MS), LEMD2 (Affinity Capture-MS), SCAMP4 (Affinity Capture-MS), ZMPSTE24 (Affinity Capture-MS)

ESM2 similar proteins: A0A140LIJ0, A1L3G9, A4IFL1, B9X187, O18968, O70491, P08033, P08034, P28230, P35212, P36380, P51915, P60572, Q02738, Q059Y8, Q0V8E7, Q1LXZ7, Q28FG4, Q29559, Q4QR83, Q5E9Z5, Q5FVF4, Q5FWS4, Q5JW98, Q5R7B4, Q5T197, Q5T1A1, Q60HF7, Q640M6, Q6GMB1, Q6WGK6, Q7SY10, Q7TNJ0, Q8BXV2, Q8C2L6, Q8C9E8, Q8CE93, Q8CEG0, Q8N5C1, Q8NDZ6

Diamond homologs: O07592, O14169, P10908, P9WMU2, P9WMU3, Q3T0T0, Q640M6, Q7L5L3, Q8N9F7, Q8WTR4, Q95JR7, Q99LY2, Q9CRY7, Q9HCC8, Q9JL55, Q9JL56, Q9NZC3, A0A8F4N283, P09394, P37965, P47625, P54527, P75367, Q06282, Q08959, Q3KTM2, Q6W3E5, Q8RB32, Q9ESM6, P47535, P55427, P75212, Q3TT99, O07244, O30405, Q9FGT9, Q9LVN0, Q9SD81, P9WLF0, P9WLF1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	97
Likely benign	7
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

3668 predictions. Top by Δscore:

Variant	Effect	Δscore
11:75436932:GTACC:G	donor_loss	1.0000
11:75436933:TAC:T	donor_loss	1.0000
11:75436934:A:AG	donor_loss	1.0000
11:75436935:C:A	donor_loss	1.0000
11:75439877:A:AC	donor_gain	1.0000
11:75439878:C:CC	donor_gain	1.0000
11:75441306:AGTCC:A	acceptor_gain	1.0000
11:75441307:GTCC:G	acceptor_gain	1.0000
11:75441308:TCC:T	acceptor_gain	1.0000
11:75441308:TCCCT:T	acceptor_loss	1.0000
11:75441309:CC:C	acceptor_gain	1.0000
11:75441309:CCC:C	acceptor_gain	1.0000
11:75441310:CC:C	acceptor_gain	1.0000
11:75441311:C:CC	acceptor_gain	1.0000
11:75441312:T:G	acceptor_loss	1.0000
11:75441313:G:C	acceptor_gain	1.0000
11:75441800:TGAC:T	acceptor_gain	1.0000
11:75441804:C:CC	acceptor_gain	1.0000
11:75441804:CTGC:C	acceptor_loss	1.0000
11:75441805:T:A	acceptor_loss	1.0000
11:75442357:CCTCA:C	donor_loss	1.0000
11:75442358:CTCA:C	donor_loss	1.0000
11:75442359:TCAC:T	donor_loss	1.0000
11:75442360:CAC:C	donor_loss	1.0000
11:75442361:A:AC	donor_gain	1.0000
11:75442361:A:T	donor_loss	1.0000
11:75442362:C:CC	donor_gain	1.0000
11:75442578:CAGT:C	acceptor_gain	1.0000
11:75442582:C:CC	acceptor_gain	1.0000
11:75443075:ACT:A	donor_gain	1.0000

AlphaMissense

3930 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:75477655:C:A	W27C	0.997
11:75477655:C:G	W27C	0.997
11:75477657:A:G	W27R	0.997
11:75477657:A:T	W27R	0.997
11:75477651:G:T	R29S	0.993
11:75477656:C:G	W27S	0.993
11:75436955:C:A	K550N	0.992
11:75436955:C:G	K550N	0.992
11:75443286:G:C	S266R	0.992
11:75443286:G:T	S266R	0.992
11:75444414:T:G	S266R	0.992
11:75441797:A:G	W392R	0.991
11:75441797:A:T	W392R	0.991
11:75443142:G:C	F314L	0.991
11:75443142:G:T	F314L	0.991
11:75443144:A:G	F314L	0.991
11:75477642:G:T	R32S	0.990
11:75477647:T:C	Y30C	0.990
11:75477674:C:T	G21D	0.990
11:75477684:A:G	C18R	0.990
11:75441218:A:T	V473D	0.989
11:75436947:A:G	L553P	0.987
11:75477648:A:G	Y30H	0.987
11:75477659:C:G	R26P	0.986
11:75477665:C:T	G24D	0.986
11:75477666:C:G	G24R	0.986
11:75477675:C:G	G21R	0.986
11:75477663:A:G	C25R	0.985
11:75443243:G:T	R281S	0.984
11:75462885:T:A	E41V	0.984

dbSNP variants (sampled 300 via entrez): RS1000066289 (11:75437204 G>A,T), RS1000069973 (11:75453931 C>T), RS1000081678 (11:75473453 A>G), RS1000099884 (11:75442901 C>A,T), RS1000215386 (11:75498892 C>T), RS1000229585 (11:75492425 A>G), RS1000243428 (11:75522217 C>T), RS1000251512 (11:75438443 C>T), RS1000310694 (11:75472881 G>A,T), RS1000320346 (11:75438079 G>A), RS1000324475 (11:75455673 A>C), RS1000373438 (11:75505066 G>A), RS1000409528 (11:75506460 C>A), RS1000446128 (11:75462031 A>T), RS1000467429 (11:75446419 G>A)

Disease associations

OMIM: gene MIM:609632 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST003209_12	Colorectal or endometrial cancer	4.000000e-06
GCST005194_155	Coronary artery disease	6.000000e-06
GCST008839_426	Height	2.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004230	endometrial neoplasm

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression, increases methylation	6
bisphenol A	affects expression, affects cotreatment, increases methylation, decreases methylation, increases expression	5
Tetrachlorodibenzodioxin	decreases expression	3
sodium arsenite	increases expression	2
Estradiol	affects cotreatment, increases expression	2
Hydrogen Peroxide	affects expression	2
Valproic Acid	affects expression, increases expression	2
Aflatoxin B1	decreases expression, increases methylation	2
Genistein	increases expression	2
aristolochic acid I	increases expression	1
bisphenol F	increases expression	1
beta-lapachone	decreases expression	1
o,p’-DDT	increases expression	1
sulforaphane	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
benzo(e)pyrene	decreases methylation	1
aflatoxin B2	increases methylation	1
CGP 52608	affects binding, increases reaction	1
entinostat	increases expression	1
bisphenol S	increases expression	1
Resveratrol	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Acetaminophen	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Azathioprine	decreases expression	1
Diethylnitrosamine	decreases expression	1
Diethylstilbestrol	increases expression	1
Glycerylphosphorylcholine	affects abundance	1
Methapyrilene	decreases methylation	1
Niclosamide	increases expression	1

Clinical trials (associated diseases)

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