The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_000180.4(GUCY2D):c.839C>G (p.Thr280Arg)

CA287523615

808220 (ClinVar)

Gene: GUCY2D
Condition: GUCY2D-related recessive retinopathy
Inheritance Mode: Autosomal recessive inheritance
UUID: 897efc9b-c34f-4e7d-b398-d71cb148f5d2
Approved on: 2025-01-31
Published on: 2025-01-31

HGVS expressions

NM_000180.4:c.839C>G
NM_000180.4(GUCY2D):c.839C>G (p.Thr280Arg)
NC_000017.11:g.8003969C>G
CM000679.2:g.8003969C>G
NC_000017.10:g.7907287C>G
CM000679.1:g.7907287C>G
NC_000017.9:g.7848012C>G
NG_009092.1:g.6300C>G
ENST00000254854.5:c.839C>G
ENST00000254854.4:c.839C>G
NM_000180.3:c.839C>G
More

Likely Pathogenic

Met criteria codes 5
PP1 PP3 PP4 PM2_Supporting PM3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Leber Congenital Amaurosis/early onset Retinal Dystrophy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for GUCY2D Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Leber Congenital Amaurosis/early onset Retinal Dystrophy VCEP
The NM_000180.4(GUCY2D):c.839C>G (p.Thr280Arg) variant predicts the substitution of arginine for threonine at position p.280. While the REVEL score is indeterminate (0.58) and does not support a deleterious effect on protein structure, the splicing impact predictor SpliceAI gives a score of 0.46 which is above the ClinGen LCA/eoRD VCEP recommended threshold of ≥0.2 and predicts a damaging impact on splicing (PP3). This variant is absent from gnomAD v4.1.0 (PM2_Supporting) and has been reported in at least 2 unrelated probands with early-onset severe retinal dystrophy who were homozygous for the variant. (1 point, PMIDs: 2642740, 29068479, PM3). 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 homozygous state (PP1; PMID: 29068479). At least one proband harboring this variant exhibits a phenotype including diagnosis of LCA (0.5 pts), significantly reduced rod ERG (0.5 pts) and extinguished cone ERG (1 pt), decreased peripheral vision (1 pt) and decreased visual acuity (1 pt). The patient's OCT showed retinal structure preserved relative to vision loss (1 pt). (Total points 5.0, PP4). In summary, this variant meets the criteria to be classified as Likely Pathogenic for GUCY2D-related recessive retinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen LCA/eoRD VCEP: PM3, PP1, PP3, PP4, PM2 supporting. (VCEP specifications version 1.0.0; date of approval 01/22/2025).
Met criteria codes
PP1
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 homozygous state (PP1; PMID: 29068479).
PP3
The splicing impact predictor SpliceAI gives a score of 0.46 which is above the ClinGen LCA / eoRD VCEP recommended threshold of ≥0.2 and predicts a damaging impact on splicing (PP3).
PP4
At least one proband harboring this variant exhibits a phenotype including diagnosis of LCA (0.5 pts), significantly reduced rod ERG (0.5 pts) and extinguished cone ERG (1 pt), decreased peripheral vision (1 pt) and visual acuity (1 pt). OCT showed retinal structure preserved relative to vision loss (1 pt). Total points 5.0, PP4. (Patient is undergoing gene therapy and may be considered for PP4_Moderate depending on the outcome.)
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting).
PM3
This variant has been reported in at least 2 unrelated probands with early-onset severe retinal dystrophy who were homozygous for the variant. 1 point, PMIDs: 2642740, 29068479 (PM3)
Curation History
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