GDPD1

Summary

GDPD1 (glycerophosphodiester phosphodiesterase domain containing 1, HGNC:20883) is a protein-coding gene on chromosome 17q22, encoding Lysophospholipase D GDPD1 (Q8N9F7). Hydrolyzes lysoglycerophospholipids to produce lysophosphatidic acid (LPA) and the corresponding amines.

This gene encodes a member of the glycerophosphodiester phosphodiesterase family of enzymes that catalyze the hydrolysis of deacylated glycerophospholipids to glycerol phosphate and alcohol. The encoded protein is localized to the cytoplasm and concentrates near the perinuclear region. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 284161 — RefSeq curated summary.

At a glance

• Gene–disease (curated): retinitis pigmentosa (Limited, GenCC)
• GWAS associations: 3
• Clinical variants (ClinVar): 45 total
• MANE Select transcript: NM_182569

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20883
Approved symbol	GDPD1
Name	glycerophosphodiester phosphodiesterase domain containing 1
Location	17q22
Locus type	gene with protein product
Status	Approved
Aliases	FLJ37451, GDE4
Ensembl gene	ENSG00000153982
Ensembl biotype	protein_coding
OMIM	616317
Entrez	284161

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 3 protein_coding, 3 nonsense_mediated_decay, 1 retained_intron

ENST00000284116, ENST00000578026, ENST00000579020, ENST00000579076, ENST00000581140, ENST00000581276, ENST00000583543

RefSeq mRNA: 3 — MANE Select: NM_182569 NM_001165993, NM_001165994, NM_182569

CCDS: CCDS11616, CCDS58583, CCDS58584

Canonical transcript exons

ENST00000284116 — 10 exons

Exon	Start	End
ENSE00001207700	59257122	59257240
ENSE00001223848	59248740	59248785
ENSE00001290351	59273651	59275970
ENSE00002705847	59220511	59220751
ENSE00003527891	59257751	59257840
ENSE00003528025	59272785	59272836
ENSE00003539263	59270936	59270995
ENSE00003549185	59245414	59245549
ENSE00003663601	59267041	59267174
ENSE00003668404	59234492	59234534

Expression profiles

Bgee: expression breadth ubiquitous, 217 present calls, max score 93.58.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.0508 / max 188.6881, expressed in 1330 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
161950	4.9184	1269
161951	0.9240	381
161952	0.2084	109

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
Brodmann (1909) area 23	UBERON:0013554	93.58	gold quality
endothelial cell	CL:0000115	90.90	gold quality
Brodmann (1909) area 46	UBERON:0006483	90.73	gold quality
cortical plate	UBERON:0005343	88.57	gold quality
primary visual cortex	UBERON:0002436	87.80	gold quality
ganglionic eminence	UBERON:0004023	86.74	gold quality
postcentral gyrus	UBERON:0002581	86.03	gold quality
prefrontal cortex	UBERON:0000451	85.91	gold quality
superior frontal gyrus	UBERON:0002661	85.55	gold quality
occipital lobe	UBERON:0002021	85.13	gold quality
middle temporal gyrus	UBERON:0002771	84.98	gold quality
parietal lobe	UBERON:0001872	84.45	gold quality
pons	UBERON:0000988	84.24	gold quality
entorhinal cortex	UBERON:0002728	83.23	gold quality
frontal cortex	UBERON:0001870	82.81	gold quality
jejunal mucosa	UBERON:0000399	82.50	gold quality
neocortex	UBERON:0001950	82.18	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.16	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	82.15	gold quality
cerebral cortex	UBERON:0000956	81.83	gold quality
Brodmann (1909) area 9	UBERON:0013540	81.32	gold quality
palpebral conjunctiva	UBERON:0001812	80.59	gold quality
ventricular zone	UBERON:0003053	80.50	gold quality
cerebellar vermis	UBERON:0004720	80.24	gold quality
lateral nuclear group of thalamus	UBERON:0002736	80.13	gold quality
bronchial epithelial cell	CL:0002328	79.91	gold quality
eye	UBERON:0000970	79.52	gold quality
cerebellum	UBERON:0002037	79.46	gold quality
cerebellar cortex	UBERON:0002129	79.12	gold quality
duodenum	UBERON:0002114	78.98	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.55
E-GEOD-111727	no	140.74
E-GEOD-137537	no	3.46

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

97 targeting GDPD1, 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-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-150-5P	99.99	66.69	1976
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-3682-5P	99.93	67.97	1163
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-6508-5P	99.92	70.67	2465

Literature-anchored findings (GeneRIF, showing 4)

• A novel splice variant of the gene is mainly expressed in human ovary and small intestine. (PMID:14612981)
• 3-D model provides the structural information; subcellular localization is in the cytoplasm; over-expression of GDE4 did not induce neurite formation or change cell morphology (PMID:18991142)
• Structural Variants Create New Topological-Associated Domains and Ectopic Retinal Enhancer-Gene Contact in Dominant Retinitis Pigmentosa. (PMID:33022222)
• Development of a selective fluorescence-based enzyme assay for glycerophosphodiesterase family members GDE4 and GDE7. (PMID:34673020)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	gdpd1	ENSDARG00000017261
mus_musculus	Gdpd1	ENSMUSG00000061666
rattus_norvegicus	Gdpd1	ENSRNOG00000060561

Paralogs (5): GDE1 (ENSG00000006007), GDPD3 (ENSG00000102886), GDPD2 (ENSG00000130055), GDPD5 (ENSG00000158555), GDPD4 (ENSG00000178795)

Protein

Protein identifiers

Lysophospholipase D GDPD1 — Q8N9F7 (reviewed: Q8N9F7)

Alternative names: Glycerophosphodiester phosphodiesterase 4, Glycerophosphodiester phosphodiesterase domain-containing protein 1

All UniProt accessions (4): Q8N9F7, J3KTA9, J3QQN7, J3QRR6

UniProt curated annotations — full annotation on UniProt →

Function. Hydrolyzes lysoglycerophospholipids to produce lysophosphatidic acid (LPA) and the corresponding amines. Shows a preference for 1-O-alkyl-sn-glycero-3-phosphocholine (lyso-PAF), lysophosphatidylethanolamine (lyso-PE) and lysophosphatidylcholine (lyso-PC). May be involved in bioactive N-acylethanolamine biosynthesis from both N-acyl-lysoplasmenylethanolamin (N-acyl-lysoPlsEt) and N-acyl-lysophosphatidylethanolamin (N-acyl-lysoPE). In addition, hydrolyzes glycerophospho-N-acylethanolamine to N-acylethanolamine. Does not display glycerophosphodiester phosphodiesterase activity, since it cannot hydrolyze either glycerophosphoinositol or glycerophosphocholine.

Subcellular location. Cytoplasm. Membrane. Perinuclear region. Endoplasmic reticulum.

Tissue specificity. Widely expressed with high expression level in testis.

Activity regulation. Lysophospholipase D activity is increased by magnesium and manganese and inhibited by calcium in a concentration dependent manner. Loss of lysophospholipase D activity by addition of EDTA.

Similarity. Belongs to the glycerophosphoryl diester phosphodiesterase family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q8N9F7-1	1	yes
Q8N9F7-2	2
Q8N9F7-3	3, UGPQ

RefSeq proteins (3): NP_001159465, NP_001159466, NP_872375* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR017946	PLC-like_Pdiesterase_TIM-brl	Homologous_superfamily
IPR030395	GP_PDE_dom	Domain
IPR052271	GDPD-Related	Family

Pfam: PF03009

Enzyme classification (BRENDA):

• EC 3.1.4.46 — glycerophosphodiester phosphodiesterase (BRENDA: 38 organisms, 62 substrates, 23 inhibitors, 29 Km, 19 kcat entries)

Substrate kinetics (BRENDA)

10 substrates with measured Km, best-characterized 10. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
BIS(P-NITROPHENYL) PHOSPHATE	0.12–3.95	5
GLYCEROPHOSPHOCHOLINE	0.036–2	5
P-NITROPHENYL PHOSPHATE	0.12–49	5
GLYCEROPHOSPHOETHANOLAMINE	0.2–0.22	3
GLYCEROPHOSPHOGLYCEROL	0.2–0.62	3
BIS(P-NITROPHENYL PHOSPHATE)	3.5–7	2
GLYCEROPHOSPHOINOSITOL	0.39	2
GLYCEROPHOSPHOSERINE	0.66	2
BIS(4-NITROPHENYL) PHOSPHATE	3.56	1
BIS(GLYCEROPHOSPHO)GLYCEROL	0.6	1

Catalyzed reactions (Rhea), 12 shown:

• 1-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine + H2O = 1-(9Z-octadecenoyl)-sn-glycero-3-phosphate + choline + H(+) (RHEA:38915)
• 1-hexadecanoyl-sn-glycero-3-phosphocholine + H2O = 1-hexadecanoyl-sn-glycero-3-phosphate + choline + H(+) (RHEA:38975)
• a 1-O-alkyl-sn-glycero-3-phosphocholine + H2O = a 1-O-alkyl-sn-glycero-3-phosphate + choline + H(+) (RHEA:39927)
• 1-O-hexadecyl-sn-glycero-3-phosphocholine + H2O = 1-O-hexadecyl-sn-glycero-3-phosphate + choline + H(+) (RHEA:41143)
• N-hexadecanoyl-sn-glycero-3-phosphoethanolamine + H2O = N-hexadecanoylethanolamine + sn-glycerol 3-phosphate + H(+) (RHEA:45436)
• N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-1-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine + H2O = N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-ethanolamine + 1-(9Z-octadecenoyl)-sn-glycero-3-phosphate + H(+) (RHEA:45544)
• N,1-dihexadecanoyl-sn-glycero-3-phosphoethanolamine + H2O = N-hexadecanoylethanolamine + 1-hexadecanoyl-sn-glycero-3-phosphate + H(+) (RHEA:45592)
• N-hexadecanoyl-1-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine + H2O = N-hexadecanoylethanolamine + 1-(9Z-octadecenoyl)-sn-glycero-3-phosphate + H(+) (RHEA:53168)
• 1-hexadecanoyl-sn-glycero-3-phosphoethanolamine + H2O = 1-hexadecanoyl-sn-glycero-3-phosphate + ethanolamine + H(+) (RHEA:53172)
• 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, splice variant 3, binding site 3, transmembrane region 2, chain 1, sequence conflict 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N9F7-F1	96.12	0.93

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): 72; 74; 87

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-6814848	Glycerophospholipid catabolism

MSigDB gene sets: 162 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_DN, GSE45365_NK_CELL_VS_CD8A_DC_DN, GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, TGACCTY_ERR1_Q2, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_DN, WTGAAAT_UNKNOWN, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, GOBP_ORGANOPHOSPHATE_CATABOLIC_PROCESS, GOBP_GLYCEROPHOSPHOLIPID_METABOLIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS, GOBP_GLYCEROPHOSPHOLIPID_CATABOLIC_PROCESS

GO Biological Process (4): glycerophospholipid catabolic process (GO:0046475), N-acylethanolamine metabolic process (GO:0070291), lipid metabolic process (GO:0006629), phospholipid metabolic process (GO:0006644)

GO Molecular Function (4): phosphatidylcholine lysophospholipase A1 activity (GO:0004622), phosphoric diester hydrolase activity (GO:0008081), metal ion binding (GO:0046872), hydrolase activity (GO:0016787)

GO Cellular Component (5): endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), membrane (GO:0016020), perinuclear region of cytoplasm (GO:0048471), cytoplasm (GO:0005737)

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	3
cytoplasm	2
glycerophospholipid metabolic process	1
phospholipid catabolic process	1
glycerolipid catabolic process	1
primary alcohol metabolic process	1
primary metabolic process	1
lipid metabolic process	1
organophosphate metabolic process	1
lysophospholipase A1 activity	1
phosphoric ester hydrolase activity	1
cation binding	1
catalytic activity	1
endomembrane system	1
intracellular membrane-bounded organelle	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

866 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GDPD1	ENPP2	Q13822	989
GDPD1	ENPP3	O14638	924
GDPD1	ENPP1	P22413	828
GDPD1	LPAR1	P78351	785
GDPD1	LPAR6	P43657	704
GDPD1	LPAR2	Q9HBW0	702
GDPD1	LPAR4	Q99677	673
GDPD1	LPAR3	Q9UBY5	671
GDPD1	LPAR5	Q9H1C0	614
GDPD1	POU2F3	Q9UKI9	580
GDPD1	NAPEPLD	Q6IQ20	575
GDPD1	ABHD4	Q8TB40	543
GDPD1	GPI	P06744	463
GDPD1	LIPH	Q8WWY8	447
GDPD1	P2RY10	O00398	430

IntAct

17 interactions, top by confidence:

A	B	Type	Score
TSPAN5	SC5D	psi-mi:“MI:0914”(association)	0.530
GDPD1	PGK2	psi-mi:“MI:0915”(physical association)	0.400
rep	CEBPZOS	psi-mi:“MI:0914”(association)	0.350
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350
COPB2	ESYT2	psi-mi:“MI:0914”(association)	0.350
COPE	ESYT2	psi-mi:“MI:0914”(association)	0.350
VAPB	ESYT2	psi-mi:“MI:0914”(association)	0.350
H2AP	GNPAT	psi-mi:“MI:0914”(association)	0.350
PLAC9	SSNA1	psi-mi:“MI:0914”(association)	0.350
GDPD1	CP	psi-mi:“MI:0914”(association)	0.350
MFSD14A	FAM171A2	psi-mi:“MI:0914”(association)	0.350
SLC1A2	UBXN8	psi-mi:“MI:0914”(association)	0.350
SLC1A3	DDX11L8	psi-mi:“MI:0914”(association)	0.350
1C		psi-mi:“MI:0914”(association)	0.350

BioGRID (98): GDPD1 (Affinity Capture-MS), TF (Affinity Capture-MS), C3 (Affinity Capture-MS), ALB (Affinity Capture-MS), SERPINA3 (Affinity Capture-MS), ITIH2 (Affinity Capture-MS), APOA1 (Affinity Capture-MS), A2M (Affinity Capture-MS), IGHG2 (Affinity Capture-MS), IGHG1 (Affinity Capture-MS), APOA4 (Affinity Capture-MS), CP (Affinity Capture-MS), HP (Affinity Capture-MS), SERPINA1 (Affinity Capture-MS), CFB (Affinity Capture-MS)

ESM2 similar proteins: A0A193KX02, A1Y9I9, A2AV36, A4IG53, A4QP75, A5PJN5, A6QQV6, A7MBI7, B6CZ56, B6CZ62, F4ZGF2, O55137, O88587, O95050, O97972, P0C5J1, P10937, P22734, Q0VGK4, Q13057, Q1LWG4, Q3T0H0, Q3TZM9, Q3UZW7, Q4V7D6, Q4V9P6, Q5BLD8, Q5R8R3, Q5RFR7, Q5U4E8, Q5ZIB9, Q6DHN0, Q6NTR1, Q6NWX7, Q6P4Z6, Q6PCI6, Q7ZW24, Q8MIR4, Q8N7N1, Q8N9F7

Diamond homologs: A0A8F4N283, O07592, O30405, P09394, P10908, P37965, P47535, P54527, P55427, P75212, P75367, P9WLF0, P9WLF1, Q06282, Q08959, Q0VGK4, Q10003, Q3T0T0, Q3TT99, Q8N9F7, Q8RB32, Q9C907, Q9CRY7, Q9JL55, Q9JL56, Q9NZC3, Q9SD81, O14169, P9WMU2, P9WMU3, Q640M6, Q7L5L3, Q8WTR4, Q95JR7, Q99LY2, Q9HCC8, P47625, Q3KTM2, Q6W3E5, Q9FGT9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	27
Likely benign	3
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1505 predictions. Top by Δscore:

Variant	Effect	Δscore
17:59245404:A:AG	acceptor_gain	1.0000
17:59245405:T:G	acceptor_gain	1.0000
17:59245409:TTCA:T	acceptor_loss	1.0000
17:59245410:TCAGT:T	acceptor_loss	1.0000
17:59245411:CAGT:C	acceptor_loss	1.0000
17:59245412:A:AG	acceptor_gain	1.0000
17:59245412:A:C	acceptor_loss	1.0000
17:59245412:AGT:A	acceptor_gain	1.0000
17:59245412:AGTGC:A	acceptor_gain	1.0000
17:59245413:G:GG	acceptor_gain	1.0000
17:59245413:GT:G	acceptor_gain	1.0000
17:59245413:GTG:G	acceptor_gain	1.0000
17:59245413:GTGC:G	acceptor_gain	1.0000
17:59245413:GTGCG:G	acceptor_gain	1.0000
17:59245545:ACTGT:A	donor_gain	1.0000
17:59245546:CTGT:C	donor_gain	1.0000
17:59245548:GT:G	donor_gain	1.0000
17:59245548:GTGTA:G	donor_loss	1.0000
17:59245549:TG:T	donor_loss	1.0000
17:59245550:G:GC	donor_loss	1.0000
17:59245550:G:GG	donor_gain	1.0000
17:59245551:TAAG:T	donor_loss	1.0000
17:59267038:TAGAA:T	acceptor_gain	1.0000
17:59267039:A:AG	acceptor_gain	1.0000
17:59267040:G:GG	acceptor_gain	1.0000
17:59267040:GA:G	acceptor_gain	1.0000
17:59267172:GAA:G	donor_gain	1.0000
17:59267175:G:GG	donor_gain	1.0000
17:59270991:GATCT:G	donor_gain	1.0000
17:59270996:G:GG	donor_gain	1.0000

AlphaMissense

2055 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:59220742:C:G	H45D	0.999
17:59220746:G:C	R46P	0.999
17:59272817:T:C	L268P	0.999
17:59272826:G:C	R271P	0.999
17:59273660:T:A	W278R	0.999
17:59273660:T:C	W278R	0.999
17:59220744:C:A	H45Q	0.998
17:59220744:C:G	H45Q	0.998
17:59257213:A:C	K153N	0.998
17:59257213:A:T	K153N	0.998
17:59257779:G:C	R172P	0.998
17:59257796:T:A	W178R	0.998
17:59257796:T:C	W178R	0.998
17:59273714:G:T	G296W	0.998
17:59273715:G:A	G296E	0.998
17:59234514:T:A	N55K	0.997
17:59234514:T:G	N55K	0.997
17:59257212:A:T	K153I	0.997
17:59273694:C:A	A289D	0.997
17:59273724:C:T	T299I	0.997
17:59273726:G:C	D300H	0.997
17:59220742:C:A	H45N	0.996
17:59220745:C:A	R46S	0.996
17:59220749:G:A	G47E	0.996
17:59245415:G:C	A63P	0.996
17:59245450:C:A	D74E	0.996
17:59245450:C:G	D74E	0.996
17:59245451:T:C	C75R	0.996
17:59245453:C:G	C75W	0.996
17:59273742:T:C	L305P	0.996

dbSNP variants (sampled 300 via entrez): RS1000053340 (17:59270528 G>A,T), RS1000068923 (17:59223210 T>G), RS1000093152 (17:59255550 T>C), RS1000122213 (17:59272374 C>G), RS1000177400 (17:59230468 C>T), RS1000220547 (17:59247400 C>A,T), RS1000246258 (17:59237234 A>G), RS1000264764 (17:59259353 G>A,C), RS1000345733 (17:59244466 G>A,C), RS1000386668 (17:59252102 C>G), RS1000417684 (17:59244200 G>T), RS1000527002 (17:59251021 A>C,G), RS1000555481 (17:59246988 G>A), RS1000607881 (17:59246585 T>A,C), RS1000614634 (17:59258477 A>G)

Disease associations

OMIM: gene MIM:616317 | disease phenotypes: MIM:213300, MIM:249000

GenCC curated gene-disease

Disease	Classification	Inheritance
retinitis pigmentosa	Limited	Autosomal dominant

Mondo (3): Joubert syndrome (MONDO:0018772), Meckel syndrome (MONDO:0018921), retinitis pigmentosa (MONDO:0019200)

Orphanet (2): Isolated Joubert syndrome (Orphanet:475), Meckel syndrome (Orphanet:564)

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST007267_241	Systolic blood pressure	2.000000e-08
GCST010002_126	Refractive error	7.000000e-42
GCST012277_18	Clostridioides difficle infection	3.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0006335	systolic blood pressure
EFO:0009130	clostridium difficile infection

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D012174	Retinitis Pigmentosa	C11.270.684; C11.768.585.658.500; C16.320.290.684

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases expression	6
trichostatin A	affects cotreatment, decreases expression, increases expression	3
Nickel	decreases expression	2
aristolochic acid I	decreases expression	1
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
propionaldehyde	increases expression	1
pirinixic acid	affects binding, increases activity, increases expression	1
bisphenol A	increases methylation	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	increases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
pentanal	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases expression, affects cotreatment	1
nutlin 3	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
(+)-JQ1 compound	increases expression	1
MT19c 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	increases expression	1
Acetaminophen	decreases expression	1
Aldehydes	increases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	affects methylation	1
Cadmium	decreases expression	1
Camptothecin	increases expression	1
Dactinomycin	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00717080	PHASE4	COMPLETED	The Role of Capsular Tension Ring (CTR) in Anterior Capsular Contraction
NCT00000114	PHASE3	COMPLETED	Randomized Trial of Vitamin A and Vitamin E Supplementation for Retinitis Pigmentosa
NCT00000116	PHASE3	COMPLETED	Randomized Trial of DHA for Retinitis Pigmentosa Patients Receiving Vitamin A
NCT00346333	PHASE3	COMPLETED	Clinical Trial of Lutein for Patients With Retinitis Pigmentosa Receiving Vitamin A
NCT01786395	PHASE3	TERMINATED	Phase III Efficacy and Safety Clinical Study of UF-021 for Treatment of Retinitis Pigmentosa
NCT04224207	PHASE3	COMPLETED	Management of Retinitis Pigmentosa by Mesenchymal Stem Cells by Wharton’s Jelly Derived Mesenchymal Stem Cells
NCT04636853	PHASE3	COMPLETED	CB-PRP in Retinitis Pigmentosa and Dry Age-related Macular Degeneration
NCT05537220	PHASE3	ACTIVE_NOT_RECRUITING	Oral N-acetylcysteine for Retinitis Pigmentosa
NCT05800301	PHASE3	COMPLETED	Management of Retinitis Pigmentosa Via Combination of Wharton’s Jelly-derived Mesenchymal Stem Cells and Magnovision
NCT05926583	PHASE3	ACTIVE_NOT_RECRUITING	A Study of AAV5-hRKp.RPGR for the Treatment of Japanese Participants With X-linked Retinitis Pigmentosa
NCT06388200	PHASE3	ACTIVE_NOT_RECRUITING	A Phase 3 Study Of OCU400 Gene Therapy for the Treatment Of Retinitis Pigmentosa
NCT07082855	PHASE3	NOT_YET_RECRUITING	A Multicenter, Randomized, Double-Blind, Controlled Clinical Study of Minocycline for the Treatment of Retinitis Pigmentosa
NCT07290530	PHASE3	NOT_YET_RECRUITING	24-Month Trial of NPI-001 for the Preservation of Photoreceptors in Retinitis Pigmentosa Associated With Usher Syndrome
NCT00100230	PHASE2	COMPLETED	DHA and X-Linked Retinitis Pigmentosa
NCT00447980	PHASE2	COMPLETED	A Study of Encapsulated Cell Technology (ECT) Implant for Participants With Early Stage Retinitis Pigmentosa
NCT00447993	PHASE2	COMPLETED	A Study of Encapsulated Cell Technology (ECT) Implant for Patients With Late Stage Retinitis Pigmentosa
NCT01233609	PHASE2	COMPLETED	Trial of Oral Valproic Acid for Retinitis Pigmentosa
NCT01399515	PHASE2	COMPLETED	Efficacy and Safety of Oral Valproic Acid for Retinitis Pigmentosa
NCT01530659	PHASE2	COMPLETED	Retinal Imaging in CNTF -Releasing Encapsulated Cell Implant Treated Patients for Early-stage Retinitis Pigmentosa
NCT01560715	PHASE2	COMPLETED	Autologous Bone Marrow-Derived Stem Cells Transplantation For Retinitis Pigmentosa
NCT02609165	PHASE2	COMPLETED	Nerve Growth Factor Eye Drops Treatment in Patients With Retinitis Pigmentosa and Cystoid Macular Edema
NCT02661711	PHASE2	COMPLETED	Aflibercept for Macular Oedema With Underlying Retinitis Pigmentosa (AMOUR) Study
NCT02804360	PHASE2	UNKNOWN	Intravitreal Dexamethasone Implant in Retinitis Pigmentosa-related Macular Edema- a Retrospective Study
NCT02837640	PHASE2	UNKNOWN	Studying a Potential Protective Effect of L-Dopa on Retinitis Pigmentosa
NCT03073733	PHASE2	COMPLETED	Safety and Efficacy of Intravitreal Injection of Human Retinal Progenitor Cells in Adults With Retinitis Pigmentosa
NCT04068207	PHASE2	COMPLETED	Minocycline Treatment in Retinitis Pigmentosa
NCT04356716	PHASE2	COMPLETED	Sildenafil for Treatment of Choroidal Ischemia
NCT04604899	PHASE2	COMPLETED	Safety of Repeat Intravitreal Injection of Human Retinal Progenitor Cells (jCell) in Adult Subjects With Retinitis Pigmentosa
NCT04763369	PHASE2	UNKNOWN	Investigation of Therapeutic Efficacy and Safety of UMSCs for the Management of Retinitis Pigmentosa (RP)
NCT04864496	PHASE2	UNKNOWN	Effects of Treatment With N- Acetylcysteine on Visual Outcomes in Patients With Retinitis Pigmentosa
NCT04945772	PHASE2	COMPLETED	Efficacy and Safety of MCO-010 Optogenetic Therapy in Adults With Retinitis Pigmentosa [RESTORE]
NCT05085964	PHASE2	TERMINATED	An Open-Label Extension Study to Evaluate Safety & Tolerability of QR-421a in Subjects With Retinitis Pigmentosa
NCT05392179	PHASE2	COMPLETED	A Study in Subjects With Retinitis Pigmentosa
NCT06627179	PHASE2	RECRUITING	Study to Evaluate Ultevursen in Subjects With Retinitis Pigmentosa (RP) Due to Mutations in Exon 13 of the USH2A Gene
NCT06628947	PHASE2	RECRUITING	A Phase II Study of Intravitreal KIO-301 in Patients With Late-stage Retinitis Pigmentosa
NCT06912633	PHASE2	RECRUITING	Safety of a Single, Intravitreal Injection of 6.0M jCell (Famzeretcel) in Retinitis Pigmentosa (RP)
NCT00063765	PHASE1	COMPLETED	Evaluation of Safety of Ciliary Neurotrophic Factor Implants in the Eye
NCT00065455	PHASE1	COMPLETED	Investigating the Effect of Vitamin A Supplementation on Retinitis Pigmentosa
NCT00458575	PHASE1	TERMINATED	A Study to Evaluate the Safety of CNTO 2476 in Patients With Advanced Retinitis Pigmentosa
NCT01068561	PHASE1	COMPLETED	Autologous Bone Marrow-Derived Stem Cells Transplantation For Retinitis Pigmentosa