RD3

RD3 regulator of GUCY2D

Basic information

Region (hg38): 1:211476521-211492162

Previous symbols: [ "C1orf36" ]

Links

ENSG00000198570 ∙ NCBI:343035 ∙ OMIM:180040 ∙ HGNC:19689 ∙ Uniprot:Q7Z3Z2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Leber congenital amaurosis 12 (Moderate), mode of inheritance: AR
• Leber congenital amaurosis 12 (Strong), mode of inheritance: AR
• Leber congenital amaurosis (Supportive), mode of inheritance: AD
• Leber congenital amaurosis 12 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Leber congenital amaurosis 12	AR	General	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	Ophthalmologic	17186464; 20301475; 22531706; 23308101

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RD3 gene.

• Leber congenital amaurosis 12 (189 variants)
• Leber congenital amaurosis (19 variants)
• not provided (9 variants)
• not specified (4 variants)
• Inborn genetic diseases (4 variants)
• Abnormality of the eye (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RD3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	29	2	32
missense			65	2	3	70
nonsense	3					3
start loss			2			2
frameshift	2					2
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region			2			2
non coding			72	8	9	89
Total	6	0	140	39	14

Highest pathogenic variant AF is 0.0000131

Variants in RD3

This is a list of pathogenic ClinVar variants found in the RD3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-211476533-C-A		Leber congenital amaurosis 12	Likely benign (Jan 13, 2018)
1-211476555-T-A		Leber congenital amaurosis 12	Uncertain significance (Jan 12, 2018)
1-211476572-G-A		Leber congenital amaurosis 12	Uncertain significance (Jan 13, 2018)
1-211476585-T-G		Leber congenital amaurosis 12	Uncertain significance (Jan 12, 2018)
1-211476634-T-C		Leber congenital amaurosis 12	Uncertain significance (Jan 13, 2018)
1-211476706-G-A		Leber congenital amaurosis 12	Uncertain significance (Jan 13, 2018)
1-211476719-C-T		Leber congenital amaurosis 12	Uncertain significance (Jan 12, 2018)
1-211476725-G-A		Leber congenital amaurosis 12	Uncertain significance (Jan 13, 2018)
1-211476789-T-A		Leber congenital amaurosis 12	Uncertain significance (Jan 12, 2018)
1-211476898-A-G		Leber congenital amaurosis 12	Uncertain significance (Jan 13, 2018)
1-211476938-C-T		Leber congenital amaurosis 12	Uncertain significance (Jan 13, 2018)
1-211476955-G-A		Leber congenital amaurosis 12	Uncertain significance (Jan 13, 2018)
1-211477029-C-T		Leber congenital amaurosis 12	Uncertain significance (Jan 13, 2018)
1-211477053-G-A		Leber congenital amaurosis 12	Uncertain significance (Jan 12, 2018)
1-211477324-C-T		Leber congenital amaurosis 12	Uncertain significance (Jan 13, 2018)
1-211477364-G-A		Leber congenital amaurosis 12	Uncertain significance (Jan 12, 2018)
1-211477384-G-A		Leber congenital amaurosis 12	Uncertain significance (Jan 13, 2018)
1-211477387-A-G		Leber congenital amaurosis 12	Benign (Jan 13, 2018)
1-211477402-C-T		Leber congenital amaurosis 12	Uncertain significance (Jan 12, 2018)
1-211477452-TC-T		Leber congenital amaurosis	Uncertain significance (Jun 14, 2016)
1-211477453-CA-C		Leber congenital amaurosis	Uncertain significance (Jun 14, 2016)
1-211477453-C-CA		Leber congenital amaurosis	Uncertain significance (Jun 14, 2016)
1-211477481-A-G		Leber congenital amaurosis 12	Uncertain significance (Jan 13, 2018)
1-211477483-G-A		Leber congenital amaurosis 12	Uncertain significance (Jan 12, 2018)
1-211477693-C-G		Leber congenital amaurosis 12	Benign (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RD3	protein_coding	protein_coding	ENST00000367002	2	16396

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000257	0.326	125731	0	12	125743	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.608	110	129	0.850	0.00000906	1233
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000646	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000805	0.0000791
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.450
• rvis_EVS: 1.13
• rvis_percentile_EVS: 92.19

Haploinsufficiency Scores

• pHI: 0.250
• hipred: N
• hipred_score: 0.333

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.274

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rd3
• Phenotype: vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: visual perception;response to stimulus;retina development in camera-type eye
• Molecular function: protein binding