Variant: NM_000329.3(RPE65):c.1338G>T (p.Arg446Ser)

CA340742354

427864 (ClinVar)

Gene: RPE65

Condition: RPE65-related recessive retinopathy

Inheritance Mode: Autosomal recessive inheritance

UUID: 79b802a8-f024-4536-a8a2-3e73fddaa67c

HGVS expressions

NM_000329.3:c.1338G>T
NM_000329.3(RPE65):c.1338G>T (p.Arg446Ser)
NC_000001.11:g.68431282C>A
CM000663.2:g.68431282C>A
NC_000001.10:g.68896965C>A
CM000663.1:g.68896965C>A
NC_000001.9:g.68669553C>A
NG_008472.1:g.23678G>T
NG_008472.2:g.23678G>T
ENST00000262340.6:c.1338G>T
ENST00000262340.5:c.1338G>T
NM_000329.2:c.1338G>T

Pathogenic

• Met criteria codes: PP1 PVS1 PP4_Moderate PM3_Strong PM2_Supporting

• Not Met criteria codes: PS3 PP3

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 RPE65 Version 1.0.0

Evidence submitted by expert panel

Leber Congenital Amaurosis/early onset Retinal Dystrophy VCEP

NM_000329.3(RPE65):c.1338G>T is a missense variant that substitutes arginine with serine at position 446. The variant is found in multiple probands affected with early-onset severe retinal dystrophy. At least one patient genotyped by whole exome sequencing (2 pts) has a diagnosis of Leber congenital amaurosis (0.5 pts) with infantile onset (1 pt), reduced visual acuity (1 pt), nyctalopia (required, 0.5 pts), light gazing (1 pt), nystagmus (1 pt), RPE mottling (0.5 pt), attenuated retinal vessels (0.5 pt), and flat rod (0.5 pts) and cone (1 pt) ERG responses, which together are highly specific for RPE65-related recessive retinopathy (9.5 pts, PMID: 30870047, PP4_Moderate). At least 3 reported probands harbor the variant in the homozygous state, while an additional proband harbors this maternal variant in compound heterozygosity with a paternal c.361dup (p.Ser121Phefs*10 variant (previously classified pathogenic by the ClinGen LCA/eoRD VCEP)(PMID: 30870047, PM3_Strong). Three pairs of siblings have been reported (PMID: 30870047) harboring the variant in either the homozygous or compound heterozygous state (PP1). This variant has a Grpmax Filtering AF of 0.000009610 (2/34488, with no homozygotes) in the Latino/Admixed American population in gnomAD v2.1.1 which is lower than the ClinGen LCA/eoRD VCEP PM2_Supporting threshold of <0.0002. Although the meta-predictor REVEL gives a score of 0.571, which is below the ClinGen LCA/eoRD VCEP PP3 threshold of >0.7, the computational splicing predictor SpliceAI indicates that the variant triggers the loss of a splice donor site, with a change score of 0.45. The variant was confirmed to exhibit a complete splicing defect in two minigene assays relative to the wild-type control, showing skipping of the 95-bp exon 12, indicating that it triggers nonsense-mediated decay (PMID: 30996589, PMID: 28714225, PVS1). In summary, this variant meets the criteria to be classified as Pathogenic for RPE65-related recessive retinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen LCA/eoRD VCEP: PVS1, PM2_Supporting, PM3_Strong, PP1, PP4_Moderate. (VCEP specifications version 1.0.0; date of approval 09/21/2023)

Met criteria codes

• PP1: Three pairs of siblings have been reported (PMID: 30870047) harboring the variant in either the homozygous or compound heterozygous state, all meeting the required phenotypes of nyctalopia and undetectable rod ERG.
• PVS1: The computational splicing predictor SpliceAI indicates that the variant triggers the loss of a splice donor site, with a change score of 0.45, which is higher than the ClinGen LCA/eoRD VCEP PP3 threshold of 0.2. The variant was confirmed to exhibit a complete splicing defect in two minigene assays relative to the wild-type control, showing skipping of the 95-bp exon 12, indicating that it triggers nonsense-mediated decay (PMID: 30996589, PMID: 28714225, PVS1).
• PP4_Moderate: At least one proband harboring this paternal variant has been found by exome sequencing to lack another genetic cause (2 pt) for diagnosis with Leber congenital amaurosis (0.5 pts) with infantile onset (1 pt), reduced visual acuity (1 pt), nyctalopia (required, 0.5 pts), light gazing (1 pt), nystagmus (1 pt), RPE mottling (0.5 pt), attenuated retinal vessels (0.5 pt), and flat rod (0.5 pts) and cone (1 pt) ERG responses, which together are highly specific for RPE65-related recessive retinopathy (9.5 pts, PMID: 30870047, PP4_Moderate).
• PM3_Strong: At least 3 reported probands harbor the variant in the homozygous state (PMID: 30870047) and meet the required phenotypes of nyctalopia and absent rod ERG response (1 pt). Proband RPCR-XVI-1 harbors this maternal variant in compound heterozygosity with a paternal c.361dup (p.Ser121Phefs*10 variant (previously classified as Pathogenic by the LCA/eoRD VCEP) and meets the required phenotypes (1 pt, PM3_Strong). Additional probands are reported with the variant in the compound heterozygous state, including in trans with p.Gly140Glu (PMID: 30870047), which was not considered to avoid circularity.
• PM2_Supporting: This variant has aGrpmax Filtering AF of 0.000009610 (2/34488) in the Latino / Admixed American population in gnomAD v2.1.1 (with no homozygotes). This allele frequency is lower than the ClinGen LCA/eoRD VCEP threshold (<0.0002) for this criterion (PM2_Supporting).

Not Met criteria codes

• PS3: The variant exhibited a complete splicing defect in two minigene assays relative to the wild-type control, showing skipping of the 95-bp exon 12, indicating that it triggers nonsense-mediated decay (PMID: 30996589, PMID: 28714225). While this evidence is eligible for PS3_Supporting, it has been combined with in silico data to meet the PVS1 code instead.
• PP3: The meta-predictor REVEL gives a score of 0.571, which is below the ClinGen LCA/eoRP VCEP PP3 threshold of >0.7 and does not predict a damaging effect on RPE65 function. The computational splicing predictor SpliceAI indicates that the variant triggers the loss of a splice donor site, with a change score of 0.45, which is higher than the ClinGen LCA/eoRP VCEP PP3 threshold of 0.2. While this evidence is eligible for PP3, it has been combined with experimental evidence confirming a complete splicing defect to meet the PVS1 code instead.

Approved on: 2024-02-20

Published on: 2024-02-20