PRCD

Summary

PRCD (photoreceptor disc component, HGNC:32528) is a protein-coding gene on chromosome 17q25.1, encoding Photoreceptor disk component PRCD (Q00LT1). Involved in vision.

This gene is predominantly expressed in the retina, and mutations in this gene are the cause of autosomal recessive retinal degeneration in both humans and dogs. Alternatively spliced transcript variants have been found for this gene.

Source: NCBI Gene 768206 — RefSeq curated summary.

At a glance

• Gene–disease (curated): retinitis pigmentosa 36 (Definitive, GenCC) — +1 more curated relationship
• GWAS associations: 2
• Clinical variants (ClinVar): 6 total — 1 pathogenic
• GTEx eGene: eQTL in 36 tissues, sQTL in 23 (q < 0.05)
• Phenotypes (HPO): 35
• Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity no evidence
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.84 (unconstrained)
• MANE Select transcript: NM_001077620

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32528
Approved symbol	PRCD
Name	photoreceptor disc component
Location	17q25.1
Locus type	gene with protein product
Status	Approved
Aliases	RP36
Ensembl gene	ENSG00000214140
Ensembl biotype	protein_coding
OMIM	610598
Entrez	768206

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 10 protein_coding_CDS_not_defined, 3 protein_coding, 1 retained_intron

MANE Select: ENST00000592014

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 2, TSL 2: 2, TSL 3: 3, TSL 4: 2, TSL 5: 4

ENST00000592014, ENST00000397630, ENST00000397633, ENST00000465808, ENST00000586148, ENST00000587063, ENST00000587289, ENST00000587813, ENST00000590555, ENST00000591317, ENST00000592340, ENST00000592432, ENST00000593023, ENST00001143418

RefSeq mRNA: 1 — MANE Select: NM_001077620 NM_001077620

CCDS: CCDS42382

Canonical transcript exons

ENST00000592014 — 5 exons

Exon	Start	End
ENSE00001529466	76543803	76545376
ENSE00001649319	76540044	76540215
ENSE00002838652	76543029	76543121
ENSE00003560166	76542553	76542633
ENSE00003582824	76540505	76540573

Expression profiles

Bgee: expression breadth ubiquitous, 196 present calls, max score 95.15.

FANTOM5 (CAGE): breadth broad, TPM avg 5.0495 / max 5210.3187, expressed in 271 samples.

Highest expression (Bgee): hemisphere of cerebellum, cerebellar hemisphere, cerebellar cortex, C1 segment of cervical spinal cord, cerebellum.

Genetic regulation across tissues (GTEx eQTL / sQTL)

PRCD is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 36 tissues and its splicing (sQTL) in 23 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 59 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Nerve Tibial	sqtl	9.6e-35	-0.89	17:76544835:A:C
Adipose Subcutaneous	sqtl	4.2e-29	-0.79	17:76544835:A:C
Brain Cerebellar Hemisphere	sqtl	4.5e-28	+1.27	17:76547597:C:G
Lung	eqtl	1.9e-25	+0.39	17:76544835:A:C
Heart Atrial Appendage	eqtl	5.2e-20	+0.32	17:76544835:A:C
Nerve Tibial	eqtl	4.3e-18	+0.38	17:76544835:A:C
Breast Mammary Tissue	sqtl	9.3e-17	-0.75	17:76544835:A:C
Muscle Skeletal	eqtl	8.2e-15	+0.33	17:76544835:A:C
Adipose Subcutaneous	eqtl	9.2e-15	+0.28	17:76544835:A:C
Brain Cerebellum	sqtl	2.9e-13	+1.11	17:76546135:C:T
Skin Sun Exposed Lower leg	eqtl	4.2e-13	+0.26	17:76544835:A:C
Brain Cerebellar Hemisphere	eqtl	7.5e-12	-0.30	17:76545047:A:G
Colon Sigmoid	eqtl	4.2e-11	+0.32	17:76545055:C:T
Thyroid	eqtl	7.1e-11	+0.27	17:76544835:A:C
Brain Cerebellum	eqtl	8.1e-11	+0.32	17:76558657:C:G
Breast Mammary Tissue	eqtl	1.5e-10	+0.26	17:76564487:G:A
Spleen	eqtl	2.0e-10	+0.39	17:76550857:C:T
Adipose Visceral Omentum	sqtl	7.9e-10	-0.65	17:76544835:A:C
Skin Sun Exposed Lower leg	sqtl	6.2e-09	-0.56	17:76544835:A:C
Skin Not Sun Exposed Suprapubic	sqtl	7.5e-09	-0.64	17:76544835:A:C

FANTOM5 promoters

showing 10 of 12 alternative TSS:

Promoter ID	TPM avg	Samples expressed
162865	1.8964	109
162866	1.8766	112
162864	0.6390	92
162856	0.3894	14
162855	0.0740	23
162862	0.0555	27
162859	0.0400	6
162863	0.0284	14
162857	0.0232	6
162858	0.0171	6

Top tissues by expression

showing 100 of 250 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	95.15	gold quality
cerebellar hemisphere	UBERON:0002245	94.74	gold quality
cerebellar cortex	UBERON:0002129	94.51	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	94.35	gold quality
cerebellum	UBERON:0002037	92.98	gold quality
spinal cord	UBERON:0002240	92.26	gold quality
substantia nigra	UBERON:0002038	86.93	gold quality
Brodmann (1909) area 9	UBERON:0013540	86.22	gold quality
midbrain	UBERON:0001891	85.25	gold quality
hypothalamus	UBERON:0001898	85.02	gold quality
right atrium auricular region	UBERON:0006631	84.15	gold quality
cardiac muscle of right atrium	UBERON:0003379	84.12	silver quality
endocervix	UBERON:0000458	84.07	gold quality
right frontal lobe	UBERON:0002810	83.88	gold quality
cardiac atrium	UBERON:0002081	83.70	gold quality
corpus callosum	UBERON:0002336	83.28	gold quality
spleen	UBERON:0002106	82.67	gold quality
apex of heart	UBERON:0002098	82.23	gold quality
inferior vagus X ganglion	UBERON:0005363	82.07	gold quality
putamen	UBERON:0001874	82.06	gold quality
prefrontal cortex	UBERON:0000451	82.05	gold quality
Ammon’s horn	UBERON:0001954	81.96	gold quality
subcutaneous adipose tissue	UBERON:0002190	81.86	gold quality
amygdala	UBERON:0001876	81.75	gold quality
omental fat pad	UBERON:0010414	81.70	gold quality
peritoneum	UBERON:0002358	81.63	gold quality
left ventricle myocardium	UBERON:0006566	81.37	gold quality
anterior cingulate cortex	UBERON:0009835	81.36	gold quality
ectocervix	UBERON:0012249	81.29	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	81.22	gold quality
tibial nerve	UBERON:0001323	80.98	gold quality
adipose tissue of abdominal region	UBERON:0007808	80.57	gold quality
body of uterus	UBERON:0009853	80.51	gold quality
frontal cortex	UBERON:0001870	80.13	gold quality
brain	UBERON:0000955	79.81	gold quality
pigmented layer of retina	UBERON:0001782	79.77	gold quality
neocortex	UBERON:0001950	79.07	gold quality
cerebral cortex	UBERON:0000956	79.00	gold quality
small intestine Peyer’s patch	UBERON:0003454	78.98	gold quality
right lobe of thyroid gland	UBERON:0001119	78.97	gold quality
left uterine tube	UBERON:0001303	78.95	gold quality
mucosa of stomach	UBERON:0001199	78.72	gold quality
heart	UBERON:0000948	78.28	gold quality
caudate nucleus	UBERON:0001873	78.19	gold quality
heart left ventricle	UBERON:0002084	78.18	gold quality
left ovary	UBERON:0002119	78.13	gold quality
sural nerve	UBERON:0015488	78.09	gold quality
forebrain	UBERON:0001890	78.00	gold quality
cardiac ventricle	UBERON:0002082	77.71	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	77.50	gold quality
right ovary	UBERON:0002118	77.43	gold quality
muscle layer of sigmoid colon	UBERON:0035805	77.29	gold quality
uterine cervix	UBERON:0000002	77.22	gold quality
right coronary artery	UBERON:0001625	77.11	gold quality
lower esophagus muscularis layer	UBERON:0035833	77.11	gold quality
lower esophagus	UBERON:0013473	77.03	gold quality
left lobe of thyroid gland	UBERON:0001120	76.71	gold quality
adipose tissue	UBERON:0001013	76.64	gold quality
temporal lobe	UBERON:0001871	76.24	gold quality
left coronary artery	UBERON:0001626	76.20	gold quality
small intestine	UBERON:0002108	76.18	gold quality
thyroid gland	UBERON:0002046	76.00	gold quality
subthalamic nucleus	UBERON:0001906	75.86	gold quality
lymph node	UBERON:0000029	75.80	gold quality
ovary	UBERON:0000992	75.52	gold quality
coronary artery	UBERON:0001621	75.49	gold quality
calcaneal tendon	UBERON:0003701	75.46	gold quality
vagina	UBERON:0000996	75.30	gold quality
myocardium	UBERON:0002349	75.10	silver quality
nucleus accumbens	UBERON:0001882	75.08	gold quality
right uterine tube	UBERON:0001302	74.76	gold quality
stromal cell of endometrium	CL:0002255	74.66	gold quality
postcentral gyrus	UBERON:0002581	74.60	gold quality
primary visual cortex	UBERON:0002436	74.48	gold quality
endothelial cell	CL:0000115	74.18	silver quality
upper lobe of left lung	UBERON:0008952	74.17	gold quality
gastrocnemius	UBERON:0001388	74.10	gold quality
skin of leg	UBERON:0001511	74.05	gold quality
right lung	UBERON:0002167	74.05	gold quality
muscle of leg	UBERON:0001383	73.91	gold quality
transverse colon	UBERON:0001157	73.84	gold quality
superficial temporal artery	UBERON:0001614	73.82	silver quality
Brodmann (1909) area 46	UBERON:0006483	73.82	gold quality
minor salivary gland	UBERON:0001830	73.77	gold quality
mucosa of transverse colon	UBERON:0004991	73.58	gold quality
esophagus	UBERON:0001043	73.54	gold quality
anatomical system	UBERON:0000467	73.37	gold quality
skin of abdomen	UBERON:0001416	73.36	gold quality
upper lobe of lung	UBERON:0008948	73.12	gold quality
material anatomical entity	UBERON:0000465	73.07	gold quality
multicellular organism	UBERON:0000468	73.07	gold quality
parietal lobe	UBERON:0001872	73.05	gold quality
body of stomach	UBERON:0001161	73.01	gold quality
fundus of stomach	UBERON:0001160	72.95	gold quality
occipital lobe	UBERON:0002021	72.87	gold quality
hindlimb stylopod muscle	UBERON:0004252	72.62	gold quality
intestine	UBERON:0000160	72.61	gold quality
gall bladder	UBERON:0002110	72.35	gold quality
tendon	UBERON:0000043	72.33	gold quality
saliva-secreting gland	UBERON:0001044	72.31	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-7316	yes	61.35
E-ANND-3	no	0.00

HPA expression

RNA tissue specificity: Tissue enriched

showing 60 of 68 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM
Retina	tissue	44.6
Choroid plexus	tissue	5.2
Cerebellum	tissue	3.3
Superior colliculi	tissue	3.1
Locus coeruleus	tissue	2.1
Cerebral cortex	tissue	1.9
Cingulate cortex	tissue	1.9
Postcentral gyrus	tissue	1.8
Hypothalamus	tissue	1.7
Pons	tissue	1.5
Motor cortex	tissue	1.5
Putamen	tissue	1.5
Thalamus	tissue	1.5
Temporal cortex	tissue	1.5
Hippocampal formation	tissue	1.4
Insular cortex	tissue	1.4
Entorhinal cortex	tissue	1.3
Somatosensory cortex	tissue	1.3
Prefrontal cortex	tissue	1.2
Hippocampus	tissue	1.2
Olfactory bulb	tissue	1.2
Septum	tissue	1.2
Nucleus accumbens	tissue	1.1
Substantia nigra	tissue	1.0
Spleen	tissue	1.0
Periaqueductal gray	tissue	1.0
Occipital cortex	tissue	1.0
Midbrain	tissue	0.9
Medulla oblongata	tissue	0.9
Vagina	tissue	0.8
Spinal cord	tissue	0.8
Retrosplenial cortex	tissue	0.7
Lymph node	tissue	0.6
Ventral pallidum	tissue	0.6
Salivary gland	tissue	0.5
Basal ganglia	tissue	0.5
Amygdala	tissue	0.5
Corpus callosum	tissue	0.5
Adrenal gland	tissue	0.5
Skin 1	tissue	0.4
Heart muscle	tissue	0.4
Ovary	tissue	0.4
Adipose tissue	tissue	0.4
Skeletal muscle	tissue	0.4
Endometrium 1	tissue	0.4
Placenta	tissue	0.4
Lung	tissue	0.4
Duodenum	tissue	0.4
Testis	tissue	0.3
Seminal vesicle	tissue	0.3
Pancreas	tissue	0.3
Prostate	tissue	0.3
Appendix	tissue	0.3
Cervix	tissue	0.2
Parathyroid gland	tissue	0.2
Colon	tissue	0.2
Small intestine	tissue	0.2
Gallbladder	tissue	0.2
Tonsil	tissue	0.2
Pituitary gland	tissue	0.1

Brain sub-regions (HPA Brain Atlas): detected in 189; highest nTPM — Vermis (7.7), Flocculonodular lobe (7.1), Cerebellar cortex (6.4), Principal sensory trigeminal nucleus (5.0), Nucleus raphe magnus (4.6).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting PRCD by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 57 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-3617-3P	99.98	67.86	918
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-22-3P	99.93	68.13	917
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-3934-3P	99.76	65.51	1351
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-646	99.68	67.84	1645
HSA-MIR-3679-3P	99.64	69.88	1599
HSA-MIR-1260A	99.61	66.67	1098
HSA-MIR-1260B	99.61	66.67	1098
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-6733-3P	99.54	67.80	1281
HSA-MIR-6081	99.48	66.07	1446
HSA-MIR-3123	99.47	67.15	2693
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-4505	99.27	67.81	2678
HSA-MIR-5787	99.22	67.86	2628
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-6734-3P	99.15	66.27	1627
HSA-MIR-4478	99.07	65.16	2320
HSA-MIR-5001-5P	99.05	66.76	1972
HSA-MIR-3619-5P	99.00	68.87	2308
HSA-MIR-6876-3P	98.97	65.69	765
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-4711-5P	98.89	68.00	965

Functional genomics

gnomAD constraint: pLI 1.25e-05, LOEUF 1.84, missense Z 0.422 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000592014 — one region, missense o/e 0.84. ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 3)

• The identification of a second pathogenic mutation of PRCD in multiple retinitis pigmentosa (RP) patients confirms the role of PRCD in the aetiology of RP in humans. (PMID:20507925)
• The identification of a third mutation in PRCD confirms its role in the pathogenesis of retinitis pigmentosa. (PMID:23805042)
• Disrupting PRCD palmitoylation eliminating the modified cysteine dramatically affects the stability of PRCD. (PMID:27613864)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Prcd	ENSMUSG00000075410
rattus_norvegicus	Prcd	ENSRNOG00000090755

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:3649529) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 8 distinct phenotype terms.

Mouse phenotype (MP)	Records
abnormal photoreceptor outer segment morphology	1
abnormal retina pigment epithelium morphology	1
retina rod cell degeneration	1
abnormal retina rod cell outer segment morphology	1
thin retina outer nuclear layer	1
increased microglial cell activation	1
abnormal photoreceptor outer segment disc membrane morphology	1
abnormal photoreceptor outer segment diameter	1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Bos taurus	E1B7R9	87.0%	Diamond
Canis lupus familiaris	Q00LT9	85.2%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
ST6GALNAC2	protein-coding	10610
CYGB	protein-coding	114757
ST6GALNAC1	protein-coding	55808
SNORD1A	snoRNA	677848
SNORD1B	snoRNA	677849
SNORD1C	snoRNA	677850
RHBDF2	protein-coding	79651
SNHG16	ncRNA	100507246
AANAT	protein-coding	15
UBE2O	protein-coding	63893
SPHK1	protein-coding	8877

Protein

Protein identifiers

Photoreceptor disk component PRCD — Q00LT1 (reviewed: Q00LT1)

Alternative names: Progressive rod-cone degeneration protein

All UniProt accessions (1): Q00LT1

UniProt curated annotations — full annotation on UniProt →

Function. Involved in vision.

Subunit / interactions. Interacts with RHO/rhodopsin; the interaction promotes PRCD stability.

Subcellular location. Cell projection. Cilium. Photoreceptor outer segment. Membrane. Endoplasmic reticulum. Golgi apparatus.

Post-translational modifications. Palmitoylated at Cys-2. Palmitoylation is essential for protein stability and trafficking to the photoreceptor outer segment, but does not appear to be essential for membrane localization. Probably palmitoylated by ZDHHC3. Phosphorylated.

Disease relevance. Retinitis pigmentosa 36 (RP36) [MIM:610599] A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the PRCD family.

RefSeq proteins (1): NP_001071088* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027937	PRCD	Family

Pfam: PF15201

UniProt features (7 total): sequence variant 4, chain 1, region of interest 1, lipid moiety-binding region 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q00LT1-F1	65.20	0.09

Human Protein Atlas

Protein class: Predicted intracellular proteins, Disease related genes, Human disease related genes, Eye disease

Protein evidence: Evidence at protein level

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 (1)

Type	Positions
S-palmitoyl cysteine	2

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 0; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

MSigDB gene sets: 115 (showing top): GOBP_SENSORY_PERCEPTION_OF_LIGHT_STIMULUS, GOBP_RESPONSE_TO_RADIATION, GOBP_DETECTION_OF_LIGHT_STIMULUS, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS, GOBP_DETECTION_OF_ABIOTIC_STIMULUS, GOBP_DETECTION_OF_STIMULUS, GOBP_SENSORY_PERCEPTION, GOBP_DETECTION_OF_LIGHT_STIMULUS_INVOLVED_IN_SENSORY_PERCEPTION, GOCC_NEURON_PROJECTION, GOBP_RESPONSE_TO_LIGHT_STIMULUS, GOCC_CELL_PROJECTION_MEMBRANE, GOCC_PHOTORECEPTOR_OUTER_SEGMENT_MEMBRANE, GOCC_PLASMA_MEMBRANE_REGION, GOCC_CILIARY_MEMBRANE, GOCC_CILIUM

GO Biological Process (2): detection of light stimulus involved in visual perception (GO:0050908), visual perception (GO:0007601)

GO Molecular Function (1): opsin binding (GO:0002046)

GO Cellular Component (7): extracellular region (GO:0005576), cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), Golgi apparatus (GO:0005794), photoreceptor outer segment membrane (GO:0042622), photoreceptor outer segment (GO:0001750), membrane (GO:0016020)

GO top-level categories

12 GO namespaces:

Category	Terms
cellular anatomical structure	4
cytoplasm	2
endomembrane system	2
intracellular membrane-bounded organelle	2
visual perception	1
detection of light stimulus involved in sensory perception	1
sensory perception of light stimulus	1
protein binding	1
intracellular anatomical structure	1
photoreceptor outer segment	1
ciliary membrane	1
photoreceptor cell cilium	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 6 of 10 annotations. The rest are phylogenetic / computational / electronic (IEA).

6 experimentally-supported GO terms:

GO term	NS	Evidence
detection of light stimulus involved in visual perception	BP	mutant phenotype
Golgi apparatus	CC	direct assay
cytoplasm	CC	direct assay
endoplasmic reticulum	CC	direct assay
extracellular region	CC	direct assay
photoreceptor outer segment membrane	CC	direct assay

Protein interactions and networks

STRING

showing 15 of 944 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRCD	PCARE	A6NGG8	836
PRCD	IMPG2	Q9BZV3	815
PRCD	ZNF513	Q8N8E2	808
PRCD	PDE6A	P16499	802
PRCD	CNGB1	Q14028	799
PRCD	CERKL	Q49MI3	798
PRCD	EYS	Q5T1H1	797
PRCD	PDE6G	P18545	780
PRCD	IDH3B	O43837	780
PRCD	TULP1	O00294	770
PRCD	GUCA1B	Q9UMX6	770
PRCD	TTC8	Q8TAM2	765
PRCD	CNGA1	P29973	763
PRCD	FSCN2	O14926	750
PRCD	RPE65	Q16518	748

IntAct

BioGRID (3 interactions; top human partners by supporting records): CTBP2 (Affinity Capture-MS), EEA1 (Cross-Linking-MS (XL-MS)), MYH15 (Cross-Linking-MS (XL-MS))

Disease & clinical

Genetic variants

Variant evidence for PRCD: 6 ClinVar records (1 pathogenic / likely pathogenic); 2 GWAS associations. Per-variant detail is on Sugi Variant.

ClinVar

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

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

Top pathogenic / likely-pathogenic (1)

Showing all 1 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant ID	HGVS	Classification	Review	Submitters
3243136	NC_000017.10:g.(?74536224)(74538656_?)del	Pathogenic	criteria provided, single submitter	1

Per-variant reference — Sugi Variant

Explore PRCD’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 26 predictions of 331):

Position(s)	Effect	Δscore	Sites
17:76540574–76540575	donor_loss	0.9900	5
17:76540571	donor_gain	0.9800
17:76542631	donor_gain	0.9800
17:76540216–76540217	donor_loss	0.9700	6
17:76540220	donor_loss	0.9600
17:76543027–76543028	acceptor_loss	0.9600	6
17:76544015	acceptor_gain	0.9600
17:76540219	donor_loss	0.9500
17:76540218–76540220	donor_loss	0.9300	3
17:76540220	donor_loss	0.9200

AlphaMissense

59 missense substitutions predicted likely pathogenic (of 345 scored), across 20 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
C2	6	0.833	0.965
S9	5	0.910	0.988
R16	4	0.779	0.898
F19	4	0.767	0.834
T4	4	0.755	0.911
V23	4	0.675	0.803
L7	3	0.918	0.947
L8	3	0.897	0.946
L11	3	0.857	0.893
L5	3	0.799	0.867
L14	3	0.740	0.804
N21	3	0.703	0.713
T3	2	0.878	0.880
A12	2	0.829	0.961
W15	2	0.814	0.814
T10	2	0.764	0.798
M13	2	0.650	0.659
K54	2	0.564	0.564
F6	1	0.875	0.875
R17	1	0.622	0.622

HPA cancer prognostics

RNA cancer specificity: Cancer enriched (Uterine Corpus Endometrial Carcinoma)

Disease associations

OMIM: gene MIM:610598 | disease phenotypes:

GenCC curated gene-disease

2 curated gene-disease records:

Disease	Classification	Inheritance	Records
retinitis pigmentosa 36	Definitive	Autosomal recessive	4
retinitis pigmentosa	Supportive	Autosomal dominant

Genomics England panels (PanelApp)

Clinical diagnostic gene panels including this gene (1 panels, 1 green/diagnostic-grade). Confidence: green = diagnostic, amber = moderate.

1 panels:

Panel	Rating
Retinal disorders	green

Mondo (2): retinitis pigmentosa 36 (MONDO:0012523), retinitis pigmentosa (MONDO:0019200)

HPO phenotypes

35 phenotypes (HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000405	Conductive hearing impairment
HP:0000407	Sensorineural hearing impairment
HP:0000501	Glaucoma
HP:0000505	Visual impairment
HP:0000510	Rod-cone dystrophy
HP:0000512	Abnormal electroretinogram
HP:0000543	Optic disc pallor
HP:0000546	Retinal degeneration
HP:0000550	Undetectable electroretinogram
HP:0000551	Color vision defect
HP:0000563	Keratoconus
HP:0000602	Ophthalmoplegia
HP:0000608	Macular degeneration
HP:0000613	Photophobia
HP:0000618	Blindness
HP:0000639	Nystagmus
HP:0000648	Optic atrophy
HP:0000662	Nyctalopia
HP:0000842	Hyperinsulinemia
HP:0001105	Retinal atrophy
HP:0007663	Reduced visual acuity
HP:0007675	Progressive night blindness
HP:0007703	Abnormal retinal pigmentation
HP:0007737	Spicular pigmentation of the retina
HP:0007787	Posterior subcapsular cataract
HP:0007843	Attenuation of retinal blood vessels
HP:0007994	Peripheral visual field loss
HP:0008046	Abnormal retinal vascular morphology
HP:0011505	Cystoid macular edema
HP:0012426	Optic disc drusen
HP:0030466	Abnormal full-field electroretinogram
HP:0030488	Abnormal central response of multifocal electroretinogram
HP:0030610	Photoreceptor outer segment loss on macular OCT
HP:0030786	Photopsia

GWAS associations

2 associations:

Study	Trait	p-value
GCST007021_2	Type 2 diabetes nephropathy	1e-6
GCST007022_4	Type 2 diabetes nephropathy including microalbuminuria	1e-6

MeSH disease descriptors

2 disease descriptors:

Descriptor	Name	Tree numbers
D012174	Retinitis Pigmentosa	C11.270.684; C11.768.585.658.500; C16.320.290.684
C566431	Retinitis Pigmentosa 36 *(supp.)*

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Particulate Matter	increases abundance, increases expression, decreases expression	2
ferrous chloride	decreases expression	1
nutlin 3	increases expression	1
jinfukang	affects cotreatment, increases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	decreases methylation	1
Cisplatin	affects cotreatment, increases expression	1
Dactinomycin	increases expression	1
Nickel	decreases expression	1
Phthalic Acids	increases methylation	1
Smoke	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Triclosan	increases expression	1
Valproic Acid	increases methylation	1
Antirheumatic Agents	decreases expression	1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

showing 60 of 238 trials:

NCT	Phase	Status	Title
NCT00717080	Phase 4	COMPLETED	The Role of Capsular Tension Ring (CTR) in Anterior Capsular Contraction
NCT00000114	Phase 3	COMPLETED	Randomized Trial of Vitamin A and Vitamin E Supplementation for Retinitis Pigmentosa
NCT00000116	Phase 3	COMPLETED	Randomized Trial of DHA for Retinitis Pigmentosa Patients Receiving Vitamin A
NCT00346333	Phase 3	COMPLETED	Clinical Trial of Lutein for Patients With Retinitis Pigmentosa Receiving Vitamin A
NCT01786395	Phase 3	TERMINATED	Phase III Efficacy and Safety Clinical Study of UF-021 for Treatment of Retinitis Pigmentosa
NCT04224207	Phase 3	COMPLETED	Management of Retinitis Pigmentosa by Mesenchymal Stem Cells by Wharton’s Jelly Derived Mesenchymal Stem Cells
NCT04636853	Phase 3	COMPLETED	CB-PRP in Retinitis Pigmentosa and Dry Age-related Macular Degeneration
NCT05537220	Phase 3	ACTIVE_NOT_RECRUITING	Oral N-acetylcysteine for Retinitis Pigmentosa
NCT05800301	Phase 3	COMPLETED	Management of Retinitis Pigmentosa Via Combination of Wharton’s Jelly-derived Mesenchymal Stem Cells and Magnovision
NCT05926583	Phase 3	ACTIVE_NOT_RECRUITING	A Study of AAV5-hRKp.RPGR for the Treatment of Japanese Participants With X-linked Retinitis Pigmentosa
NCT06388200	Phase 3	ACTIVE_NOT_RECRUITING	A Phase 3 Study Of OCU400 Gene Therapy for the Treatment Of Retinitis Pigmentosa
NCT07082855	Phase 3	NOT_YET_RECRUITING	A Multicenter, Randomized, Double-Blind, Controlled Clinical Study of Minocycline for the Treatment of Retinitis Pigmentosa
NCT07290530	Phase 3	NOT_YET_RECRUITING	24-Month Trial of NPI-001 for the Preservation of Photoreceptors in Retinitis Pigmentosa Associated With Usher Syndrome
NCT07710196	Phase 3	NOT_YET_RECRUITING	A 24-Month Trial of NPI-001 for the Preservation of Photoreceptors in Retinitis Pigmentosa Associated With Usher Syndrome
NCT00100230	Phase 2	COMPLETED	DHA and X-Linked Retinitis Pigmentosa
NCT00447980	Phase 2	COMPLETED	A Study of Encapsulated Cell Technology (ECT) Implant for Participants With Early Stage Retinitis Pigmentosa
NCT00447993	Phase 2	COMPLETED	A Study of Encapsulated Cell Technology (ECT) Implant for Patients With Late Stage Retinitis Pigmentosa
NCT01233609	Phase 2	COMPLETED	Trial of Oral Valproic Acid for Retinitis Pigmentosa
NCT01399515	Phase 2	COMPLETED	Efficacy and Safety of Oral Valproic Acid for Retinitis Pigmentosa
NCT01530659	Phase 2	COMPLETED	Retinal Imaging in CNTF -Releasing Encapsulated Cell Implant Treated Patients for Early-stage Retinitis Pigmentosa
NCT01560715	Phase 2	COMPLETED	Autologous Bone Marrow-Derived Stem Cells Transplantation For Retinitis Pigmentosa
NCT02609165	Phase 2	COMPLETED	Nerve Growth Factor Eye Drops Treatment in Patients With Retinitis Pigmentosa and Cystoid Macular Edema
NCT02661711	Phase 2	COMPLETED	Aflibercept for Macular Oedema With Underlying Retinitis Pigmentosa (AMOUR) Study
NCT02804360	Phase 2	UNKNOWN	Intravitreal Dexamethasone Implant in Retinitis Pigmentosa-related Macular Edema- a Retrospective Study
NCT02837640	Phase 2	UNKNOWN	Studying a Potential Protective Effect of L-Dopa on Retinitis Pigmentosa
NCT03073733	Phase 2	COMPLETED	Safety and Efficacy of Intravitreal Injection of Human Retinal Progenitor Cells in Adults With Retinitis Pigmentosa
NCT04068207	Phase 2	COMPLETED	Minocycline Treatment in Retinitis Pigmentosa
NCT04356716	Phase 2	COMPLETED	Sildenafil for Treatment of Choroidal Ischemia
NCT04604899	Phase 2	COMPLETED	Safety of Repeat Intravitreal Injection of Human Retinal Progenitor Cells (jCell) in Adult Subjects With Retinitis Pigmentosa
NCT04763369	Phase 2	UNKNOWN	Investigation of Therapeutic Efficacy and Safety of UMSCs for the Management of Retinitis Pigmentosa (RP)
NCT04864496	Phase 2	UNKNOWN	Effects of Treatment With N- Acetylcysteine on Visual Outcomes in Patients With Retinitis Pigmentosa
NCT04945772	Phase 2	COMPLETED	Efficacy and Safety of MCO-010 Optogenetic Therapy in Adults With Retinitis Pigmentosa [RESTORE]
NCT05085964	Phase 2	TERMINATED	An Open-Label Extension Study to Evaluate Safety & Tolerability of QR-421a in Subjects With Retinitis Pigmentosa
NCT05392179	Phase 2	COMPLETED	A Study in Subjects With Retinitis Pigmentosa
NCT06627179	Phase 2	ACTIVE_NOT_RECRUITING	Study to Evaluate Ultevursen in Subjects With Retinitis Pigmentosa (RP) Due to Mutations in Exon 13 of the USH2A Gene
NCT06628947	Phase 2	RECRUITING	A Phase II Study of Intravitreal KIO-301 in Patients With Late-stage Retinitis Pigmentosa
NCT06912633	Phase 2	ACTIVE_NOT_RECRUITING	Safety of a Single, Intravitreal Injection of 6.0M jCell (Famzeretcel) in Retinitis Pigmentosa (RP)
NCT07796646	Phase 2	NOT_YET_RECRUITING	Study to Evaluate the Long-Term Safety of Ultevursen in Participants With Retinitis Pigmentosa (RP) Due to Mutations in Exon 13 of the USH2A Gene
NCT00063765	Phase 1	COMPLETED	Evaluation of Safety of Ciliary Neurotrophic Factor Implants in the Eye
NCT00065455	Phase 1	COMPLETED	Investigating the Effect of Vitamin A Supplementation on Retinitis Pigmentosa
NCT00458575	Phase 1	TERMINATED	A Study to Evaluate the Safety of CNTO 2476 in Patients With Advanced Retinitis Pigmentosa
NCT01068561	Phase 1	COMPLETED	Autologous Bone Marrow-Derived Stem Cells Transplantation For Retinitis Pigmentosa
NCT01482195	Phase 1	COMPLETED	Trial of Subretinal Injection of (rAAV2-VMD2-hMERTK)
NCT01531348	Phase 1	COMPLETED	Intravitreal Injection of MSCs in Retinitis Pigmentosa
NCT01543906	Phase 1	COMPLETED	Oral QLT091001 in Retinitis Pigmentosa (RP) Subjects With an Autosomal Dominant Mutation in Retinal Pigment Epithelial 65 Protein (RPE65)
NCT01604356	Phase 1	COMPLETED	Acupuncture for the Treatment of Vision Loss Due to Retinitis Pigmentosa
NCT01736059	Phase 1	ACTIVE_NOT_RECRUITING	Clinical Trial of Autologous Intravitreal Bone-marrow CD34+ Stem Cells for Retinopathy
NCT02280135	Phase 1	COMPLETED	Clinical Trial of Intravitreal Injection of Autologous Bone Marrow Stem Cells in Patients With Retinitis Pigmentosa
NCT03063021	Phase 1	COMPLETED	The FIGHT-RP1 Study
NCT03772938	Phase 1	UNKNOWN	Stem Cells Therapy in Degenerative Diseases of the Retina
NCT03944239	Phase 1	ACTIVE_NOT_RECRUITING	Safety and Efficacy of Subretinal Transplantation of Clinical Human Embryonic Stem Cell Derived Retinal Pigment Epitheliums in Treatment of Retinitis Pigmentosa
NCT03999021	Phase 1	ACTIVE_NOT_RECRUITING	FIGHT-RP 1 Extension Study
NCT04284293	Phase 1	ACTIVE_NOT_RECRUITING	CNS10-NPC for the Treatment of RP
NCT04925687	Phase 1	COMPLETED	Phase 1 Study of Intravitreal Autologous CD34+ Stem Cell Therapy for Retinitis Pigmentosa
NCT05147701	Phase 1	RECRUITING	Safety of Cultured Allogeneic Adult Umbilical Cord Derived Mesenchymal Stem Cells for NAION
NCT06291935	Phase 1	RECRUITING	Safety and Tolerability of Intravitreal Administration of VG901 in Patients With Retinitis Pigmentosa Due to Mutations in the CNGA1 Gene
NCT06319872	Phase 1	RECRUITING	The Effects of Disulfiram (Antabuse®) on Visual Acuity in Patients With Retinal Degeneration
NCT06460844	Phase 1	ACTIVE_NOT_RECRUITING	Study to Evaluate Safety of RTx-015 Injection in Retinitis Pigmentosa or Choroideremia Patients (ENVISION)
NCT06936787	Phase 1	RECRUITING	An Open-label, Dose-ascending Study of IGT001 for Retinitis Pigmentosa
NCT07774975	Phase 1	NOT_YET_RECRUITING	Safety Evaluation Study of Pitavastatin PLGA Nano-particle for Retinitis Pigmentosa