Total submissions: 3
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Clin |
RCV005053966 | SCV005687725 | pathogenic | GUCY2D-related recessive retinopathy | 2025-01-30 | reviewed by expert panel | curation | NM_000180.4(GUCY2D):c.3271C>T (p.Arg1091Ter) is a nonsense variant that introduces a premature stop codon into exon 19 of 20, and is predicted to lead to C-terminal truncation of a gene product in which loss-of-function is an established mechanism of disease (PVS1_Strong). This variant is present in gnomAD v.4.1.0 at a total allele frequency of 0.000005058, with 8 alleles / 1,581,610 total alleles, which is lower than the ClinGen LCA/eoRD VCEP PM2_Supporting threshold of <0.0004 (PM2_Supporting). This variant has been reported in 2 probands with early-onset severe retinal dystrophy who were compound heterozygous with either the NM_000180.4(GUCY2D):c.2302C>T (p.Arg768Trp) variant (suspected in trans, 0.5 points, PMID: 23847139) or the NM_000180.4(GUCY2D):c.937C>T (p.Arg313Cys) variant (confirmed in trans, 1 pt, VCEP member-provided data), both of which were previously classified either pathogenic or likely pathogenic by the ClinGen LCA / eoRD VCEP. The variant has also been reported in 1 proband diagnosed with retinitis pigmentosa with onset between ages 5-10 years with the NM_000180.4(GUCY2D):c.2516del (p.Thr839ArgfsTer27) variant suspected in trans, which was previously classified as pathogenic by the ClinGen LCA/eoRD VCEP (2 total points, VCEP member-provided data, PM3_Strong). The variant has been reported to segregate with childhood-onset severe retinal dystrophy through the proband plus 1 similarly affected relative, with the variant present in the compound heterozygous state (VCEP member-provided data, PP1). At least one proband harboring this variant exhibits a phenotype including diagnosis of Leber congenital amaurosis (0.5 pts) with congenital onset (1 pt), genotyping by a large gene panel that did not provide an alternative explanation for retinal disease (2 pts), nystagmus (1 pt), nyctalopia (0.5 pts), and undetectable electroretinogram responses from rods (0.5 pts) and cones (1.0 pt), which together are specific for GUCY2D-related recessive retinopathy (6.5 points, PMID: 23847139, PP4). The variant showed successsful rescue of rod and cone function when delivered by subretinal injection into Gucy2e−/−Gucy2f−/− knockout mouse retinas, but this model was not considered sufficient evidence of non-pathogenicity in humans so was not considered applicable for BS3 (PMID: 27881908). In vitro, guanylate cyclase activity is reduced to 25% but is not less than LCA/eoRD cutoff of <10% activity (PMID: 23035049) In summary, this variant meets the criteria to be classified as pathogenic for GUCY2D-related recessive retinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen LCA/eoRD VCEP: PVS1_Strong, PM2_Supporting, PM3_Strong, PP1, and PP4. (VCEP specifications version 1.0.0; date of approval 01/22/2025). |
| Blueprint Genetics | RCV001073763 | SCV001239323 | uncertain significance | Retinal dystrophy | 2017-12-04 | criteria provided, single submitter | clinical testing | |
| Labcorp Genetics |
RCV001388270 | SCV001589198 | pathogenic | Cone-rod dystrophy 6; Leber congenital amaurosis 1 | 2024-02-18 | criteria provided, single submitter | clinical testing | This sequence change creates a premature translational stop signal (p.Arg1091*) in the GUCY2D gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GUCY2D are known to be pathogenic (PMID: 10951519, 11328726). This variant is present in population databases (rs769818541, gnomAD 0.002%). This premature translational stop signal has been observed in individual(s) with clinical features of Leber congenital amaurosis (PMID: 17964524). ClinVar contains an entry for this variant (Variation ID: 866048). For these reasons, this variant has been classified as Pathogenic. |