GUCY2D
Basic information
Region (hg38): 17:8002615-8020342
Previous symbols: [ "CORD6", "LCA", "GUC2D", "GUC1A4" ]
Links
Phenotypes
GenCC
Source:
- Leber congenital amaurosis 1 (Definitive), mode of inheritance: AR
- cone-rod dystrophy (Supportive), mode of inheritance: AD
- Leber congenital amaurosis (Supportive), mode of inheritance: AD
- central areolar choroidal dystrophy (Supportive), mode of inheritance: AD
- cone-rod dystrophy 6 (Strong), mode of inheritance: AD
- Leber congenital amaurosis 1 (Strong), mode of inheritance: AR
- night blindness, congenital stationary, type1i (Strong), mode of inheritance: AR
- GUCY2D-related dominant retinopathy (Definitive), mode of inheritance: AD
- GUCY2D-related recessive retinopathy (Definitive), mode of inheritance: AR
- cone-rod dystrophy (Definitive), mode of inheritance: AD
- central areolar choroidal dystrophy (Limited), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Choroidal dystrophy, central areolar 1; Cone-rod dystrophy 6; Leber congenital amaurosis, type 1; Cone-Rod dystrophy, autosomal recessive; Night blindness, congenital stationary, type 1I | AD/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 | 8554074; 9097965; 9618177; 11709018; 12015276; 12325031; 12623820; 12552567; 15024725; 20006823; 20301475; 20517349; 22194653; 22695961; 29559409 |
ClinVar
This is a list of variants' phenotypes submitted to
- Cone-rod dystrophy 6;Leber congenital amaurosis 1 (56 variants)
- Leber congenital amaurosis 1 (30 variants)
- Leber congenital amaurosis 1;Cone-rod dystrophy 6 (26 variants)
- GUCY2D-related recessive retinopathy (22 variants)
- not provided (19 variants)
- Retinal dystrophy (13 variants)
- Cone-rod dystrophy 6 (7 variants)
- Leber congenital amaurosis (6 variants)
- GUCY2D-related disorder (4 variants)
- Night blindness, congenital stationary, type1i (3 variants)
- Cone-rod dystrophy 6;Leber congenital amaurosis 1;Choroidal dystrophy, central areolar, 1;Night blindness, congenital stationary, type1i (2 variants)
- Cone-rod dystrophy 6;Choroidal dystrophy, central areolar, 1;Leber congenital amaurosis 1;Night blindness, congenital stationary, type1i (2 variants)
- Choroidal dystrophy, central areolar, 1;Cone-rod dystrophy 6;Night blindness, congenital stationary, type1i;Leber congenital amaurosis 1 (2 variants)
- Choroidal dystrophy, central areolar, 1 (2 variants)
- Cone-rod dystrophy (2 variants)
- Leber congenital amaurosis 1;Night blindness, congenital stationary, type1i;Choroidal dystrophy, central areolar, 1;Cone-rod dystrophy 6 (2 variants)
- Congenital blindness (1 variants)
- POLR3-related leukodystrophy (1 variants)
- Leber congenital amaurosis 1;Choroidal dystrophy, central areolar, 1;Cone-rod dystrophy 6;Night blindness, congenital stationary, type1i (1 variants)
- not specified (1 variants)
- Night blindness, congenital stationary, type1i;Leber congenital amaurosis 1;Cone-rod dystrophy 6;Choroidal dystrophy, central areolar, 1 (1 variants)
- Night blindness, congenital stationary, type1i;Choroidal dystrophy, central areolar, 1;Cone-rod dystrophy 6;Leber congenital amaurosis 1 (1 variants)
- Optic atrophy (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GUCY2D 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 | 381 | 396 | ||||
missense | 17 | 27 | 477 | 15 | 544 | |
nonsense | 30 | 36 | ||||
start loss | 5 | |||||
frameshift | 44 | 16 | 60 | |||
inframe indel | 12 | |||||
splice donor/acceptor (+/-2bp) | 14 | 25 | ||||
splice region | 22 | 52 | 4 | 78 | ||
non coding | 153 | 17 | 173 | |||
Total | 104 | 67 | 497 | 549 | 34 |
Highest pathogenic variant AF is 0.000341
Variants in GUCY2D
This is a list of pathogenic ClinVar variants found in the GUCY2D region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
17-8002739-A-G | Benign (Jun 19, 2021) | |||
17-8002911-C-T | GUCY2D-related disorder | Likely benign (Jul 04, 2019) | ||
17-8003044-GGCAAT-G | Cone-rod dystrophy 6;Leber congenital amaurosis 1 | Pathogenic (Jan 10, 2024) | ||
17-8003048-A-G | Leber congenital amaurosis 1 • Cone-rod dystrophy 6;Leber congenital amaurosis 1 | Pathogenic (Dec 03, 2023) | ||
17-8003049-T-A | Leber congenital amaurosis 1 | Pathogenic (-) | ||
17-8003049-T-C | Retinal dystrophy | Likely pathogenic (May 27, 2024) | ||
17-8003050-G-A | Leber congenital amaurosis 1 • GUCY2D-related recessive retinopathy | Pathogenic (Jan 30, 2025) | ||
17-8003050-G-C | Leber congenital amaurosis 1 • Leber congenital amaurosis 1;Cone-rod dystrophy 6 | Pathogenic (Oct 18, 2023) | ||
17-8003054-G-T | Retinal dystrophy | Uncertain significance (Jan 01, 2023) | ||
17-8003058-G-A | Leber congenital amaurosis 1;Cone-rod dystrophy 6 | Benign (Jan 29, 2024) | ||
17-8003058-GCGCC-G | Cone-rod dystrophy 6;Leber congenital amaurosis 1 | Pathogenic (Nov 18, 2022) | ||
17-8003060-G-A | Cone-rod dystrophy 6;Leber congenital amaurosis 1 | Uncertain significance (Oct 30, 2020) | ||
17-8003063-C-T | Cone-rod dystrophy 6;Leber congenital amaurosis 1 • Inborn genetic diseases | Uncertain significance (Nov 20, 2024) | ||
17-8003071-G-T | Cone-rod dystrophy 6;Leber congenital amaurosis 1 | Likely benign (Sep 11, 2023) | ||
17-8003083-G-A | Leber congenital amaurosis 1;Cone-rod dystrophy 6 | Likely benign (Oct 19, 2023) | ||
17-8003087-C-A | Leber congenital amaurosis 1;Cone-rod dystrophy 6 | Uncertain significance (Jun 04, 2023) | ||
17-8003087-C-G | Choroidal dystrophy, central areolar, 1 • Cone-rod dystrophy 6;Leber congenital amaurosis 1 | Uncertain significance (Jul 07, 2023) | ||
17-8003089-C-T | Leber congenital amaurosis 1;Cone-rod dystrophy 6 | Likely benign (Sep 24, 2023) | ||
17-8003092-G-T | Cone-rod dystrophy 6;Leber congenital amaurosis 1 | Likely benign (Feb 09, 2023) | ||
17-8003093-C-T | Inborn genetic diseases | Uncertain significance (Mar 12, 2024) | ||
17-8003096-T-C | Cone-rod dystrophy 6;Leber congenital amaurosis 1 • Cone-rod dystrophy 6;Night blindness, congenital stationary, type1i;Leber congenital amaurosis 1;Choroidal dystrophy, central areolar, 1 | Uncertain significance (Oct 05, 2022) | ||
17-8003098-C-A | Cone-rod dystrophy 6;Leber congenital amaurosis 1 | Pathogenic (Mar 09, 2023) | ||
17-8003098-C-CGGTCCCGCGTGGTGGGCTCCGTCCCTGCCCCGCCTCCCCCGGGCCCTG | Leber congenital amaurosis 1 | Likely pathogenic (-) | ||
17-8003101-T-G | Cone-rod dystrophy 6;Leber congenital amaurosis 1 | Likely benign (Nov 25, 2023) | ||
17-8003104-C-G | Leber congenital amaurosis 1;Cone-rod dystrophy 6 | Likely benign (May 02, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
GUCY2D | protein_coding | protein_coding | ENST00000254854 | 18 | 17746 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
6.46e-10 | 0.998 | 125591 | 0 | 157 | 125748 | 0.000624 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.781 | 598 | 654 | 0.914 | 0.0000449 | 6880 |
Missense in Polyphen | 217 | 274.73 | 0.78986 | 2975 | ||
Synonymous | -0.616 | 301 | 288 | 1.05 | 0.0000205 | 2455 |
Loss of Function | 2.86 | 22 | 42.0 | 0.524 | 0.00000224 | 455 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000664 | 0.000661 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.00392 | 0.00380 |
European (Non-Finnish) | 0.000448 | 0.000440 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.000132 | 0.000131 |
Other | 0.000689 | 0.000652 |
dbNSFP
Source:
- Function
- FUNCTION: Probably plays a specific functional role in the rods and/or cones of photoreceptors. It may be the enzyme involved in the resynthesis of cGMP required for recovery of the dark state after phototransduction.;
- Disease
- DISEASE: Cone-rod dystrophy 6 (CORD6) [MIM:601777]: An inherited retinal dystrophy characterized by retinal pigment deposits visible on fundus examination, predominantly in the macular region, and initial loss of cone photoreceptors followed by rod degeneration. This leads to decreased visual acuity and sensitivity in the central visual field, followed by loss of peripheral vision. Severe loss of vision occurs earlier than in retinitis pigmentosa, due to cone photoreceptors degenerating at a higher rate than rod photoreceptors. {ECO:0000269|PubMed:12552567, ECO:0000269|PubMed:15111605, ECO:0000269|PubMed:18332321, ECO:0000269|PubMed:18487367, ECO:0000269|PubMed:20517349, ECO:0000269|PubMed:21552474, ECO:0000269|PubMed:22194653, ECO:0000269|PubMed:23734073, ECO:0000269|PubMed:24480840, ECO:0000269|PubMed:9618177, ECO:0000269|PubMed:9683616}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Choroidal dystrophy, central areolar, 1 (CACD1) [MIM:215500]: A form of central areolar choroidal dystrophy, a retinal disease that affects the macula and results in a well- demarcated circumscribed area of atrophy of the pigment epithelium and choriocapillaris. CACD1 inheritance is autosomal recessive. {ECO:0000269|PubMed:22695961}. Note=The disease may be caused by mutations affecting the gene represented in this entry.;
- Pathway
- Purine metabolism - Homo sapiens (human);Olfactory transduction - Homo sapiens (human);Phototransduction - Homo sapiens (human);Signaling by GPCR;Signal Transduction;Purine metabolism;actions of nitric oxide in the heart;Purine nucleotides nucleosides metabolism;Visual signal transduction: Rods;G alpha (i) signalling events;Inactivation, recovery and regulation of the phototransduction cascade;The phototransduction cascade;Visual phototransduction;GPCR downstream signalling;Visual signal transduction: Cones
(Consensus)
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- loftool
- 0.0925
- rvis_EVS
- -1.37
- rvis_percentile_EVS
- 4.51
Haploinsufficiency Scores
- pHI
- 0.313
- hipred
- Y
- hipred_score
- 0.626
- ghis
- 0.412
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.169
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | High | Medium | High |
Mouse Genome Informatics
- Gene name
- Gucy2e
- Phenotype
- homeostasis/metabolism 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); vision/eye phenotype;
Zebrafish Information Network
- Gene name
- gucy2d
- Affected structure
- optomotor response
- Phenotype tag
- abnormal
- Phenotype quality
- arrested
Gene ontology
- Biological process
- cGMP biosynthetic process;protein phosphorylation;signal transduction;receptor guanylyl cyclase signaling pathway;visual perception;regulation of rhodopsin mediated signaling pathway;intracellular signal transduction
- Cellular component
- nuclear outer membrane;plasma membrane;integral component of plasma membrane;photoreceptor disc membrane
- Molecular function
- peptide receptor activity;guanylate cyclase activity;protein kinase activity;protein binding;ATP binding;GTP binding;signaling receptor activity