Variant: NM_000180.4(GUCY2D):c.1979G>A (p.Arg660Gln)

CA226064

98555 (ClinVar)

Gene: GUCY2D

Condition: GUCY2D-related recessive retinopathy

Inheritance Mode: Autosomal recessive inheritance

UUID: dcb2a69f-561f-4d88-b3c4-a7f180466569

Approved on: 2025-01-30

Published on: 2025-01-30

HGVS expressions

NM_000180.4:c.1979G>A
NM_000180.4(GUCY2D):c.1979G>A (p.Arg660Gln)
NC_000017.11:g.8012472G>A
CM000679.2:g.8012472G>A
NC_000017.10:g.7915790G>A
CM000679.1:g.7915790G>A
NC_000017.9:g.7856515G>A
NG_009092.1:g.14803G>A
ENST00000254854.5:c.1979G>A
ENST00000254854.4:c.1979G>A
NM_000180.3:c.1979G>A

Uncertain Significance

• Met criteria codes: PP4 PP3 PM2_Supporting

• Not Met criteria codes: PM3

Expert Panel

Leber Congenital Amaurosis/early onset Retinal Dystrophy VCEP

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

Evidence submitted by expert panel

Leber Congenital Amaurosis/early onset Retinal Dystrophy VCEP

The NM_000180.4(GUCY2D):c.1979G>A (p.Arg660Gln) variant is predicted to replace the arginine at position p.660 with glutamine. The computational predictor REVEL gives a score of 0.655, which is above the ClinGen LCA / eoRD VCEP threshold of ≥0.644 and predicts a damaging effect on RetGC-1 protein function (PP3). At least one proband harboring this variant exhibits a phenotype including diagnosis of LCA (0.5 pts) as an infant (1 pt). On examination at age 6 years, she had nystagmus (1 pt) with visual acuities of 1/200 (1 pt). Ophthalmoscopy showed attenuated retinal vessels and a granular appearance to the fundus (0.5 pts), Visual field was limited to a central island of function (1 pt). Rod ERGs extinguished (0.5 pts), cone ERGs severely reduced (1 pt). At ages 9 and 10 years, visual acuities had declined to light perception, and there was no measurable visual field by kinetic perimetry. Together these are specific for GUCY2D-related recessive retinopathy. (6.5 points total, PMID: 12623820, PP4). This variant is present in gnomAD v.4.1.0 at a total allele frequency of 0.0003903, with 630 alleles / 1,613,968 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 at least 1 proband with early-onset severe retinal dystrophy who harbored the variant in the presumed compound heterozygous state (PMID: 21602930). However, the proband was not counted for this criterion because the other variant, p.Glu103Val, has not yet been classified and was not confirmed to be in trans with p.Arg660Gln (0 pts). PM3_Supporting requires at least 0.5 total points, so this criterion was not met. In summary, this variant meets the criteria to be classified as VUS for GUCY2D-related recessive retinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen LCA/eoRD VCEP: PM2_supporting, PP3, PP4. (VCEP specifications version 1.0.0; date of approval 01/22/2025).

Met criteria codes

• PP4: At least one proband harboring this variant exhibits a phenotype including diagnosis of LCA (0.5 pts) as an infant (1 pt). On examination at age 6 years, she had nystagmus (1 pt) with visual acuities of 1/200 (1 pt). Ophthalmoscopy showed attenuated retinal vessels and a granular appearance to the fundus (0.5 pts), Visual field was limited to a central island of function (1 pt). Rod ERGs extinguished (0.5 pts), cone ERGs severely reduced (1 pt). At ages 9 and 10 years, visual acuities had declined to light perception, and there was no measurable visual field by kinetic perimetry. Together these are specific for GUCY2D-related recessive retinopathy. (6.5 points total, PMID: 12623820, PP4)
• PP3: The computational predictor REVEL gives a score of 0.655, which is above the ClinGen LCA / eoRD VCEP threshold of ≥0.644 and predicts a damaging effect on RetGC-1 function (PP3).
• PM2_Supporting: This variant is present in gnomAD v.4.1.0 at a total allele frequency of 0.0003903, with 630 alleles / 1,613,968 total alleles, which is lower than the ClinGen LCA/eoRD VCEP PM2_Supporting threshold of <0.0004 (PM2_Supporting).

Not Met criteria codes

• PM3: This variant has been reported in at least 1 proband with early-onset severe retinal dystrophy who harbored the variant in the presumed compound heterozygous state (PMID: 21602930). However, the proband was not counted for this criterion because the other variant, p.Glu103Val, has not yet been classified and was not confirmed to be in trans with p.Arg660Gln (0 pts). PM3_Supporting requires at least 0.5 total points, so this criterion was not met.