RD3

protein-coding

RD3 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]

Previous symbols:
  • C1orf36

MANE transcript

NM_001164688.2

Inheritance

AR, AD

ClinVar variants

P:14U:94B:56

Top phenotype

Leber congenital amaurosis 12

gnomAD constraint

pLI —, LoF o/e 0.98

Max pathogenic AF

—

Genomic locus

chr1:211,476,522-211,492,162

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~15.6 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Leber congenital amaurosis 12STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012525

Submitter: Labcorp Genetics (formerly Invitae)

RD3-related retinopathyDEFINITIVE

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).

Leber congenital amaurosis 12STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012525

Submitter: PanelApp Australia

Leber congenital amaurosisSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0018998

Submitter: Orphanet

Leber congenital amaurosis 12DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0012525

Submitter: G2P

Leber congenital amaurosis 12MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0012525

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Leber congenital amaurosis 12AR

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

Refs: 17186464; 20301475; 22531706; 23308101Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RD3 variants in ClinVar

8 Conditions Cataloged
Leber congenital amaurosis 12Total: 142
not providedTotal: 46
Inborn genetic diseasesTotal: 27
not specifiedTotal: 24
RD3-related disorderTotal: 9
Retinal dystrophyTotal: 5
Leber congenital amaurosisTotal: 1
Abnormality of the eyeTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
45
clinvar
2
clinvar
49
missense
89
clinvar
7
clinvar
2
clinvar
98
nonsense
4
clinvar
1
clinvar
5
start loss
3
clinvar
3
frameshift
3
clinvar
3
clinvar
6
splice donor/acceptor (+/-2bp)
1
clinvar
2
clinvar
3
Total8694524164

Highest pathogenic variant AF is 0.000008208664

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001164688.2RefSeqNP_001158160.12MANE Select
ENST00000680073.1EnsemblENSP00000505312.12MANE Select
NM_183059.3RefSeqNP_898882.12Standard
ENST00000367002.5EnsemblENSP00000355969.42Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.6081101290.8500.000009061233
Missense (PolyPhen)3939.5250.98671393
Synonymous0.4925256.70.9170.00000380403
Loss of Function0.053077.150.9793.93e-769

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000650.000062rare
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian0.000110.00011rare
Finnish00.0absent
European (Non-Finnish)0.0000800.000079rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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