RD3
protein-codingRD3 regulator of GUCY2D
Gene summary
This gene encodes a retinal protein that is associated with promyelocytic leukemia-gene product (PML) bodies in the nucleus. Mutations in this gene cause Leber congenital amaurosis type 12, a disease that results in retinal degeneration. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]
- C1orf36
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~15.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0012525
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0700235
Submitter: ClinGen
Retinal degeneration 3 (RD3) is an evolutionarily conserved 23 kDa protein expressed in rod and cone photoreceptor cells. Mutations in the gene encoding RD3 resulting in unstable non-functional C-terminal truncated proteins are responsible for early onset photoreceptor degeneration in Leber congenital amaurosis 12 (MIM#610612). Leber congenital amaurosis (LCA) is the earliest and most severe form of all inherited retinal dystrophies (IRD) and the most frequent cause of inherited blindness in children. Leber congenital amaurosis-12 (LCA12) is an autosomal recessive form of Inherited retinal disease (IRD) and is characterized by congenital nystagmus, low vision, sluggish pupillary reflexes, absence of ocular pursuit from birth (Perrault et al., 2013) *RD3* is located at 1q32.3 and consists of 3 exons encoding a basic protein of 195 amino acids that is preferentially expressed in the retina (Aravindan S et al. 2017). It exhibits increasing expression throughout mouse early postnatal development. It is highly expressed in cone and rod outer segments, and colocalizes with GC1 and GC2. In cones, RD3 protein binds the C-terminus of GC1 and mediates its export from the endoplasmic reticulum to endosomal vesicles. GC1 and GC2 loss iis observed n photoreceptor cells of *rd3* mice expressing a truncated unstable rd3 protein. RD3 protein promotes accumulation of retinal membrane guanylyl cyclase (RetGC) in the photoreceptor outer segment and suppresses RetGC activation by guanylyl cyclase–activating proteins (GCAPs). Truncating variants in RD3 cause severe retinal disease by preventing the inhibitory interaction of RD3 with the guanylyl cyclase (Chang B et al. 1993; Friedman JS et al., 2006; Zulliger R. et al., 2016; Peshenko IV et al. 2019). RD3 also negatively regulaes RetGC by binding it and blocking activation by GCAPs. This ability of RD3 to bind and suppress RetGC is likely critical for photoreceptor survival (Peshenko IV et al. 2019). A total of 9 variants have already been identified underlying Leber congenital amaurosis 12. The mutation spectrum in *RD3* includes 4 nonsense, 3 frameshifts and 2 splice junction losses (PMID: 17186464, 22531706, 23308101). In this curation, data from 3 consanguineous families and 2 isolated individuals with 5 unique variants), were collected from 3 publications (Friedman JS, et al., 2006, PMID: 17186464, Preising MN, et al., 2012, PMID: 22531706, Perrault I, et al., 2013, PMID: 23308101). Experimental evidence for expression, biochemical function and animal model systems were calculated as well (Aravindan S, et al., 2017, PMID: 29030614, Peshenko IV, et al., 2019, PMID: 30559291, Friedman JS, et al., 2006, PMID: 17186464). In summary, *RD3* is definitively associated with RD3-related retinopathy. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This clinical validity classification was approved by the ClinGen Retina Gene Curation Expert Panel on January 4th, 2022 (SOP Version 8).
Inheritance Pattern: AR
Disease ID:MONDO:0012525
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0018998
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0012525
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0012525
Submitter: Ambry Genetics
Clinical Genomic Database (CGD)
Manifestation: Ophthalmologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to RD3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001164688.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 45 | 2 | 49 | ||
| missense | 89 | 7 | 2 | 98 | ||
| nonsense | 4 | 1 | 5 | |||
| start loss | 3 | 3 | ||||
| frameshift | 3 | 3 | 6 | |||
| splice donor/acceptor (+/-2bp) | 1 | 2 | 3 | |||
| Total | 8 | 6 | 94 | 52 | 4 | 164 |
Highest pathogenic variant AF is 0.000008208664
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001158160.1 | 2 | MANE Select | |
| Ensembl | ENSP00000505312.1 | 2 | MANE Select | |
| RefSeq | NP_898882.1 | 2 | Standard | |
| Ensembl | ENSP00000355969.4 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- visual perception
- response to stimulus
- retina development in camera-type eye
Molecular Function
- protein binding
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000367002
- Coding exons
- 2
- Length
- 16396
- Individuals with no LoFs
- 125731
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 12
- Defined
- 125743
- p
- 0.0000477
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.608 | 110 | 129 | 0.850 | 0.00000906 | 1233 |
| Missense (PolyPhen) | 39 | 39.525 | 0.98671 | 393 | ||
| Synonymous | 0.492 | 52 | 56.7 | 0.917 | 0.00000380 | 403 |
| Loss of Function | 0.0530 | 7 | 7.15 | 0.979 | 3.93e-7 | 69 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000065 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000080 | 0.000079 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.450
- RVIS EVS
- 1.13
- RVIS percentile EVS
- 92.19
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.274
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |