PDC

Summary

PDC (phosducin, HGNC:8759) is a protein-coding gene on chromosome 1q31.1, encoding Phosducin (P20941). May participate in the regulation of visual phototransduction or in the integration of photoreceptor metabolism.

This gene encodes a phosphoprotein, which is located in the outer and inner segments of the rod cells in the retina. This protein may participate in the regulation of visual phototransduction or in the integration of photoreceptor metabolism. It modulates the phototransduction cascade by interacting with the beta and gamma subunits of the retinal G-protein transducin. This gene is a potential candidate gene for retinitis pigmentosa and Usher syndrome type II. Alternatively spliced transcript variants encoding different isoforms have been identified.

Source: NCBI Gene 5132 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 30 total
• MANE Select transcript: NM_002597

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:8759
Approved symbol	PDC
Name	phosducin
Location	1q31.1
Locus type	gene with protein product
Status	Approved
Aliases	MEKA
Ensembl gene	ENSG00000116703
Ensembl biotype	protein_coding
OMIM	171490
Entrez	5132

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000391997, ENST00000497198

RefSeq mRNA: 2 — MANE Select: NM_002597 NM_002597, NM_022576

CCDS: CCDS1370, CCDS41447

Canonical transcript exons

ENST00000391997 — 4 exons

Exon	Start	End
ENSE00001842020	186461059	186461114
ENSE00001893085	186443566	186444506
ENSE00002286699	186449399	186449483
ENSE00003541722	186446426	186446577

Expression profiles

Bgee: expression breadth ubiquitous, 119 present calls, max score 89.07.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.6066 / max 497.6689, expressed in 9 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
16348	0.6066	9

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.07	gold quality
pigmented layer of retina	UBERON:0001782	66.77	gold quality
decidua	UBERON:0002450	56.55	gold quality
right hemisphere of cerebellum	UBERON:0014890	55.47	gold quality
cerebellar cortex	UBERON:0002129	55.33	gold quality
cerebellar hemisphere	UBERON:0002245	55.21	gold quality
corpus callosum	UBERON:0002336	54.31	gold quality
cerebellum	UBERON:0002037	54.20	gold quality
colonic epithelium	UBERON:0000397	54.11	silver quality
pancreatic ductal cell	CL:0002079	53.73	silver quality
calcaneal tendon	UBERON:0003701	53.40	silver quality
cortical plate	UBERON:0005343	53.00	gold quality
hair follicle	UBERON:0002073	52.43	gold quality
quadriceps femoris	UBERON:0001377	50.47	gold quality
frontal pole	UBERON:0002795	50.41	gold quality
middle frontal gyrus	UBERON:0002702	50.30	gold quality
paraflocculus	UBERON:0005351	50.18	gold quality
Brodmann (1909) area 10	UBERON:0013541	50.18	gold quality
epithelial cell of pancreas	CL:0000083	50.11	gold quality
tibialis anterior	UBERON:0001385	49.88	silver quality
vastus lateralis	UBERON:0001379	49.75	gold quality
metanephric glomerulus	UBERON:0004736	49.61	gold quality
Brodmann (1909) area 9	UBERON:0013540	49.45	gold quality
Brodmann (1909) area 46	UBERON:0006483	49.30	gold quality
cerebellar vermis	UBERON:0004720	49.25	gold quality
skin of hip	UBERON:0001554	49.21	gold quality
cervix squamous epithelium	UBERON:0006922	49.20	gold quality
tibial nerve	UBERON:0001323	49.06	gold quality
olfactory bulb	UBERON:0002264	48.92	gold quality
myocardium	UBERON:0002349	48.87	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-7316	yes	71.02
E-GEOD-137537	yes	20.52
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 7)

• Phosducin mutations are not a major cause of dominant or recessive retinitis pigmentosa, Leber congenital amaurosis, or cone-rod degeneration. (PMID:14758335)
• SUMO-1 controls the protein stability and the biological function of phosducin. (PMID:16421094)
• Candidate gene-based association studies in 2 different populations revealed several SNPs in the PDC gene to be associated with stress-dependent blood pressure phenotypes. (PMID:19959875)
• Data suggest that the existence of a common epitope on the molecules of phosducin and beta-actin may reflect a topological similarity of a small region of their surfaces. (PMID:20804785)
• identification of Pdc as a gene for stress-induced hypertension offers new insights into the relationship between sympathetic nervous system activation, blood pressure regulation and genetic factors (PMID:21191291)
• Data suggest that phosducin rs12402521 polymorphism is an important genetic predictor of obesity-related hypertension. (PMID:22365573)
• Phosducin regulates secretory activity in TT line of thyroid parafollicular C cells. (PMID:25153685)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	pdca	ENSDARG00000011886
danio_rerio	pdcb	ENSDARG00000017634
mus_musculus	Pdc	ENSMUSG00000006007
rattus_norvegicus	Pdc	ENSRNOG00000002517
drosophila_melanogaster	CG7650	FBGN0036519
caenorhabditis_elegans		WBGENE00003142

Paralogs (4): TXNDC9 (ENSG00000115514), PDCL3 (ENSG00000115539), PDCL (ENSG00000136940), PDCL2 (ENSG00000163440)

Protein

Protein identifiers

Phosducin — P20941 (reviewed: P20941)

Alternative names: 33 kDa phototransducing protein, Protein MEKA

All UniProt accessions (1): P20941

UniProt curated annotations — full annotation on UniProt →

Function. May participate in the regulation of visual phototransduction or in the integration of photoreceptor metabolism. Inhibits the transcriptional activation activity of the cone-rod homeobox CRX.

Subunit / interactions. Forms a complex with the beta and gamma subunits of the GTP-binding protein, transducin. Interacts with CRX.

Subcellular location. Cytoplasm. Cytosol. Nucleus. Cell projection. Cilium. Photoreceptor outer segment. Photoreceptor inner segment Nucleus.

Post-translational modifications. Light-induced changes in cyclic nucleotide levels modulate the phosphorylation of this protein by cAMP kinase.

Similarity. Belongs to the phosducin family.

Isoforms (3)

UniProt ID	Names	Canonical?
P20941-1	1	yes
P20941-2	2, PhLOP1
P20941-3	3

RefSeq proteins (2): NP_002588, NP_072098 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001200	Phosducin	Family
IPR023196	Phosducin_N_dom_sf	Homologous_superfamily
IPR024253	Phosducin_thioredoxin-like_dom	Domain
IPR036249	Thioredoxin-like_sf	Homologous_superfamily
IPR051499	Phosducin-like_reg	Family

Pfam: PF02114

UniProt features (10 total): region of interest 2, compositionally biased region 2, splice variant 2, chain 1, domain 1, modified residue 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P20941-F1	82.83	0.54

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): 73

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 75 (showing top): FXR_IR1_Q6, SHEPARD_BMYB_MORPHOLINO_UP, GOBP_PHOTOTRANSDUCTION, CHX10_01, GOBP_SENSORY_PERCEPTION_OF_LIGHT_STIMULUS, GOBP_RESPONSE_TO_RADIATION, KEGG_OLFACTORY_TRANSDUCTION, GOBP_DETECTION_OF_LIGHT_STIMULUS, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS, GOBP_DETECTION_OF_ABIOTIC_STIMULUS, GOBP_DETECTION_OF_STIMULUS, GFI1_01, GOBP_SENSORY_PERCEPTION, GOCC_NEURON_PROJECTION, GATA1_02

GO Biological Process (4): G protein-coupled receptor signaling pathway (GO:0007186), visual perception (GO:0007601), phototransduction (GO:0007602), regulation of G protein-coupled receptor signaling pathway (GO:0008277)

GO Molecular Function (1): phospholipase inhibitor activity (GO:0004859)

GO Cellular Component (7): photoreceptor outer segment (GO:0001750), photoreceptor inner segment (GO:0001917), nucleus (GO:0005634), cytosol (GO:0005829), cytoplasm (GO:0005737), cilium (GO:0005929), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
signal transduction	2
G protein-coupled receptor activity	1
sensory perception of light stimulus	1
detection of light stimulus	1
G protein-coupled receptor signaling pathway	1
regulation of signal transduction	1
glycerophospholipase activity	1
lipase inhibitor activity	1
photoreceptor cell cilium	1
intracellular membrane-bounded organelle	1
cytoplasm	1
intracellular anatomical structure	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1

Protein interactions and networks

STRING

766 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PDC	SUCLG2	Q96I99	934
PDC	RHO	P08100	809
PDC	PLIN2	Q99541	760
PDC	SAG	P10523	757
PDC	GNGT1	P63211	730
PDC	RCVRN	P35243	634
PDC	RPE65	Q16518	633
PDC	GNB1	P04697	607
PDC	RGS16	O15492	605
PDC	F13B	P05160	595
PDC	GHITM	Q9H3K2	581
PDC	PFN4	Q8NHR9	574
PDC	PFN3	P60673	573
PDC	CACNA1S	Q13698	552
PDC	RBP3	P10745	548

IntAct

4 interactions, top by confidence:

A	B	Type	Score
ITM2B	ILVBL	psi-mi:“MI:0914”(association)	0.350
PDC	TSPY2	psi-mi:“MI:0914”(association)	0.350
CYRIB	PDC	psi-mi:“MI:0914”(association)	0.350

BioGRID (10): PDC (Two-hybrid), PDC (Proximity Label-MS), PDC (Affinity Capture-MS), PDC (Biochemical Activity), DCC (Affinity Capture-MS), TSPY2 (Affinity Capture-MS), PLXNC1 (Affinity Capture-MS), PDC (Affinity Capture-MS), PDC (Affinity Capture-MS), PSMC5 (Two-hybrid)

ESM2 similar proteins: A0JM23, A5PMF7, B8JKF4, F4JZJ2, O23052, O60502, O77560, P0CF65, P0CI65, P19632, P20941, P20942, P41686, Q008S8, Q0P564, Q13371, Q2HJA9, Q2TBM9, Q3U213, Q568B8, Q58CZ2, Q5FVM7, Q5R7K4, Q5RCM7, Q5SNQ7, Q5ZKZ4, Q63737, Q68EV9, Q692V3, Q6AZT7, Q6P3V7, Q6P5D8, Q75BD8, Q80TN4, Q8BHD8, Q8S8L9, Q8VC33, Q8VIJ5, Q8VZQ0, Q94HV8

Diamond homologs: O77560, P19632, P20941, P20942, P41686, Q13371, Q2HJA9, Q63737, Q9DBX2, Q9QW08, Q9VUR7, Q9XS39, Q0VCW8, Q4KLJ8, Q5RB77, Q6P268, Q71A38, Q71A39, Q8BVF2, Q9H2J4, Q9Y7L1, Q12017, Q32LN3, Q78Y63, Q8MR62, Q8N4E4, O14530, O18883, O64628, Q8K581, Q9CQ79

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
GRK2	“down-regulates activity”	PDC	phosphorylation
CAMK2A	unknown	PDC	phosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	28
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

563 predictions. Top by Δscore:

Variant	Effect	Δscore
1:186444502:CTCAT:C	acceptor_gain	1.0000
1:186444504:CAT:C	acceptor_gain	1.0000
1:186444505:ATC:A	acceptor_loss	1.0000
1:186444506:TCT:T	acceptor_loss	1.0000
1:186444507:C:CC	acceptor_gain	1.0000
1:186446420:TCTTA:T	donor_loss	1.0000
1:186446421:CTTA:C	donor_loss	1.0000
1:186446422:TTAC:T	donor_loss	1.0000
1:186446423:TACC:T	donor_loss	1.0000
1:186446424:A:T	donor_loss	1.0000
1:186446425:CCTTT:C	donor_gain	1.0000
1:186446577:CCTGG:C	acceptor_loss	1.0000
1:186446578:C:CA	acceptor_loss	1.0000
1:186446578:C:CC	acceptor_gain	1.0000
1:186446579:T:A	acceptor_loss	1.0000
1:186449480:TAAT:T	acceptor_gain	1.0000
1:186444503:TCAT:T	acceptor_gain	0.9900
1:186444504:CATC:C	acceptor_gain	0.9900
1:186444505:AT:A	acceptor_gain	0.9900
1:186444508:T:A	acceptor_loss	0.9900
1:186444513:A:AC	acceptor_gain	0.9900
1:186444513:A:C	acceptor_gain	0.9900
1:186446424:A:AC	donor_gain	0.9900
1:186446425:C:CC	donor_gain	0.9900
1:186446574:GGTC:G	acceptor_gain	0.9900
1:186446575:GTC:G	acceptor_gain	0.9900
1:186446576:TC:T	acceptor_gain	0.9900
1:186446577:CC:C	acceptor_gain	0.9900
1:186446583:A:AC	acceptor_gain	0.9900
1:186449388:G:C	donor_gain	0.9900

AlphaMissense

1649 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:186444307:A:T	V138D	0.994
1:186444151:A:G	L190P	0.992
1:186444220:A:G	F167S	0.991
1:186444352:A:G	F123S	0.991
1:186444154:A:G	L189P	0.988
1:186446570:T:A	K23N	0.988
1:186446570:T:G	K23N	0.988
1:186444219:A:C	F167L	0.987
1:186444219:A:T	F167L	0.987
1:186444221:A:G	F167L	0.987
1:186444058:A:G	L221P	0.985
1:186444160:G:T	P187H	0.985
1:186446543:A:C	F32L	0.985
1:186446543:A:T	F32L	0.985
1:186446545:A:G	F32L	0.985
1:186444177:A:C	F181L	0.984
1:186444177:A:T	F181L	0.984
1:186444178:A:G	F181S	0.984
1:186444179:A:G	F181L	0.984
1:186444245:C:G	A159P	0.983
1:186444310:A:T	V137D	0.982
1:186444160:G:C	P187R	0.981
1:186446577:C:T	G21E	0.981
1:186444146:A:C	Y192D	0.979
1:186444268:A:G	L151P	0.978
1:186449399:C:G	G21R	0.978
1:186449399:C:T	G21R	0.978
1:186444276:A:C	C148W	0.977
1:186446569:C:G	G24R	0.977
1:186446569:C:T	G24R	0.977

dbSNP variants (sampled 300 via entrez): RS1000106181 (1:186452461 C>A,T), RS1000272649 (1:186461730 T>G), RS1000727469 (1:186462116 G>T), RS1000886579 (1:186449256 C>T), RS1001057236 (1:186456694 C>T), RS1001235338 (1:186449012 A>C), RS1001675422 (1:186453078 A>G), RS1001840405 (1:186447442 C>G), RS1002059727 (1:186454401 A>T), RS1002218341 (1:186450514 T>C), RS1002292672 (1:186447789 G>A,C,T), RS1002396962 (1:186443329 A>G), RS1002680019 (1:186451167 A>G), RS1002698222 (1:186450385 A>T), RS1002774950 (1:186451573 A>G,T)

Disease associations

OMIM: gene MIM:171490 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
Benzo(a)pyrene	increases methylation	1
Catechin	affects cotreatment, increases expression	1
Valproic Acid	decreases methylation	1

Clinical trials (associated diseases)

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