The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000329.3(RPE65):c.215T>C (p.Phe72Ser)

CA340748948

467826 (ClinVar)

Gene: RPE65 (HGNC:6121)
Condition: RPE65-related recessive retinopathy (MONDO:0100368)
Inheritance Mode: Autosomal recessive inheritance
UUID: b4b83bc1-846d-4f9b-90e8-c75a6baffc80
Approved on: 2026-09-22
Published on: 2026-09-22

HGVS expressions

NM_000329.3:c.215T>C
NM_000329.3(RPE65):c.215T>C (p.Phe72Ser)
NC_000001.11:g.68446740A>G
CM000663.2:g.68446740A>G
NC_000001.10:g.68912423A>G
CM000663.1:g.68912423A>G
NC_000001.9:g.68685011A>G
NG_008472.1:g.8220T>C
NG_008472.2:g.8220T>C
ENST00000262340.6:c.215T>C
ENST00000262340.5:c.215T>C
NM_000329.2:c.215T>C
More

Pathogenic

Met criteria codes 5
PM3_Strong PP3_Moderate PP1 PP4_Moderate PM2_Supporting

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 RPE65 Version 1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Leber Congenital Amaurosis/early onset Retinal Dystrophy VCEP
NM_000329.3(RPE65):c.215T>C (p.Phe72Ser) is a missense variant that replaces phenylalanine with serine at amino acid 72. This variant is present in gnomAD v.4.1.1 at a GrpMax allele frequency of 0.000009530, with 18 alleles / 1180044 total alleles in the non-Finnish European population, which is lower than the ClinGen LCA / eoRD VCEP PM2_Supporting threshold of <0.0002 (PM2_Supporting). This variant has been reported in at least 2 unrelated probands with early-onset severe retinal dystrophy who carry the NM_000329.2:c.130C>T, p.Arg44* variant, confirmed in trans, which was previously classified as pathogenic by the ClinGen LCA/eoRD VCEP. (2.0 points, VCEP member and clinical lab testing results). This variant has also been reported in at least 1 proband and a sibling with early-onset severe retinal dystrophy who are compound heterozygous, phase unknown, with the NM_000329.2:c.617T>C, p.Ile206Thr variant, previously classified as pathogenic by the ClinGen LCA / eoRD VCEP (0.25 points, VCEP member clinical lab testing results), (2.25 total points, PM3_Strong). At least one proband harboring this variant exhibits a phenotype including: absent or severely decreased rod electroretinogram (ERG) responses (0.5 pts), congenital night blindness/nyctalopia (0.5 pts), clinical diagnosis of early onset Rod Cone Dystrophy (0.5 pts), previous retinal dystrophy gene panel testing that did not provide an alternative explanation for visual impairment (2 pts), pigmentary retinopathy with attenuated vessels (0.5 pts), RPE mottling (0.5 pts), symptomatic onset between birth and five years (1 pt), OCT is preserved with respect to vision loss (1 pt), decreased peripheral vision (1 pt), abnormal color vision or evidence of cone involvement on ERG (1 pt), and decreased central visual acuity (1 pt), which together are highly specific for RPE65-related recessive retinopathy (9.5 points in total, unpublished clinical observation, PP4_Moderate). 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 (unpublished clinical evidence, PP1). The computational predictor REVEL gives a score of 0.946, which is above the ClinGen LCA/eoRD VCEP threshold of ≥0.774 and predicts a damaging effect on RPE65 function (PP3_Moderate). The splicing impact predictor SpliceAI gives a score of 0.01, which is below the ClinGen LCA / eoRD VCEP recommended threshold of ≥0.2 and does not strongly predict an impact on splicing. 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: PM2_Supporting, PM3_Strong, PP4_Moderate, PP1, PP3_Moderate. (VCEP specifications version 1.0.0).
Met criteria codes
PM3_Strong
This variant has been reported in at least 2 unrelated probands with early-onset severe retinal dystrophy who are compound heterozygous in trans with the NM_000329.3:c.130C>T, p.Arg44* variant, which was previously classified as pathogenic by the ClinGen LCA/eoRD VCEP. (2.0 points, VCEP member and clinical lab testing results). This variant has been reported in at least 1 proband and a sibling with early-onset severe retinal dystrophy who are compound heterozygous, phase unknown, with the NM_000329.3:c.617T>C, p.Ile206Thr variant, which was previously classified as pathogenic by the ClinGen LCA / eoRD VCEP (0.25 points, VCEP member clinical lab testing results). The variant is also reported in at least 1 unrelated proband with early-onset severe retinal dystrophy who is compound heterozygous with the NM_000329.3:c.308T>C. Phe103Ser, currently a variant of uncertain significance. This variant will not count in this curation so that Phe72Ser can be used to curate Phe103Ser and avoid circularity (0 points) (2.25 total points, PM3_strong).
PP3_Moderate
The computational predictor REVEL gives a score of 0.946, which is above the ClinGen LCA/eoRD VCEP threshold of ≥0.774 and predicts a damaging effect on RPE65 function. The splicing impact predictor SpliceAI gives a score of 0.01, which is below the ClinGen LCA / eoRD VCEP recommended threshold of ≥0.2 and does not strongly predict an impact on splicing (PP3_Moderate).
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 compound heterozygous state (PP1; Clinical evidence).
PP4_Moderate
At least one proband harboring this variant exhibits a phenotype including: absent or severely decreased rod electroretinogram (ERG) responses (0.5 pts), congenital night blindness/nyctalopia (0.5 pts), clinical diagnosis of early onset Rod Cone Dystrophy (0.5 pts), previous retinal dystrophy gene panel testing that did not provide an alternative explanation for visual impairment (2 pts), pigmentary retinopathy with attenuated vessels (0.5 pts), RPE mottling (0.5 pts), symptomatic onset between birth and five years (1 pt), OCT is preserved with respect to vision loss (1 pt), decreased peripheral vision (1 pt), abnormal color vision or evidence of cone involvement on ERG (1 pt), and decreased central visual acuity (1 pt), which together are highly specific for RPE65-related recessive retinopathy (9.5 points in total, unpublished clinical observation, PP4_Moderate).
PM2_Supporting
This variant is present in gnomAD v.4.1.0 at a GrpMax allele frequency of 0.000009530, with 18 alleles / 1180044 total alleles in the non-Finnish European population, which is lower than the ClinGen LCA / eoRD VCEP PM2_Supporting threshold of <0.0002 (PM2_Supporting).
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
ClinGen Terms of Use.
¤ Powered by BCM's Genboree.