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 label mismatch: RPGR vs undefined
  • 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_001034853.2(RPGR):c.922G>C (p.Ala308Pro)

CA270037

143094 (ClinVar)

Gene: RPGR (HGNC:6103)
Condition: RPGR-related retinopathy (MONDO:0100437)
Inheritance Mode: X-linked inheritance (dominant (HP:0001423))
UUID: 1ec84574-6253-4687-af4b-51eb058a0e23
Approved on: 2025-05-20
Published on: 2025-05-20

HGVS expressions

NM_001034853.2:c.922G>C
NM_001034853.2(RPGR):c.922G>C (p.Ala308Pro)
NC_000023.11:g.38304647C>G
CM000685.2:g.38304647C>G
NC_000023.10:g.38163900C>G
CM000685.1:g.38163900C>G
NC_000023.9:g.38048844C>G
NG_009553.1:g.27889G>C
ENST00000494707.6:c.126G>C
ENST00000642170.1:n.1189-3276G>C
ENST00000642395.2:c.922G>C
ENST00000642558.1:c.829G>C
ENST00000642739.1:c.922G>C
ENST00000644238.1:c.922G>C
ENST00000644337.1:c.922G>C
ENST00000645032.1:c.922G>C
ENST00000645124.1:c.922G>C
ENST00000646020.1:c.922G>C
ENST00000647261.1:c.922G>C
ENST00000318842.11:c.922G>C
ENST00000339363.7:c.922G>C
ENST00000378505.6:c.922G>C
ENST00000465127.1:c.172-361474C>G
ENST00000474584.5:c.922G>C
ENST00000482855.5:c.922G>C
ENST00000494841.1:n.185G>C
NM_000328.2:c.922G>C
NM_001034853.1:c.922G>C
NM_001367245.1:c.919G>C
NM_001367246.1:c.922G>C
NM_001367247.1:c.922G>C
NM_001367248.1:c.952G>C
NM_001367249.1:c.919G>C
NM_001367250.1:c.919G>C
NM_001367251.1:c.922G>C
NR_159803.1:n.1064G>C
NR_159804.1:n.973G>C
NR_159805.1:n.1064G>C
NR_159806.1:n.1064G>C
NR_159807.1:n.1064G>C
NR_159808.1:n.1189-3276G>C
NM_000328.3:c.922G>C
More

Likely Pathogenic

Met criteria codes 4
PM2_Supporting PP3_Moderate PP4 PP1_Moderate
Not Met criteria codes 2
PS3 PS4

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen X-linked Inherited Retinal Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RPGR Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
X-linked Inherited Retinal Disease VCEP
NM_001034853.2(RPGR):c.922G>C (p.Ala308Pro) is a missense variant encoding substitution of alanine with proline at amino acid 308. This variant is absent from hemizygous individuals in gnomAD v4.1.0 (PM2_Supporting). The computational predictor REVEL gives a score of 0.904, which is between the ClinGen X-linked IRD VCEP thresholds of 0.773 to 0.931 and predicts a damaging effect on RPGR function (PP3_moderate). The computational splicing predictor SpliceAI gives a delta score of 0.01 for acceptor gain, which is below the ClinGen X-linked IRD VCEP threshold of >0.2 and does not predict that the variant disrupts RPGR splicing. At least one proband harboring this variant exhibits a phenotype including early onset (1 pt) of night blindness (0.5 pts), decreased central visual acuity (0.5 pts), visual field constriction (0.5 pts), family history consistent with X-linked inheritance (2 pts), delayed or milder phenotype in females (1 pt), and next-generation sequencing-based genotyping identifying no alternative causes of retinal disease (2 pts), which together are specific for RPGR-related retinopathy (7.5 pts, PP4, PMID: 25324289). The variant has been reported to segregate with retinal dystrophy through at least 3 affected meioses from 1 family (PP1; PMID: 26316687, PMID: 25324289). The variant has been included in multiple publications (PMIDs: 25324289, 26316687, and 26427425), however these have reported the same family, so PS4_Supporting was not met. In summary, this variant meets the criteria to be classified as likely pathogenic for RPGR-related retinopathy based on the ClinGen X-linked Inherited Retinal Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RPGR Version 1.0.0; PM2_supporting, PP1_moderate, PP3_moderate, and PP4_supporting. (date of approval 05/16/2025).
Met criteria codes
PM2_Supporting
This variant is absent from hemizygous individuals in gnomAD v4.1.0 (PM2_Supporting).
PP3_Moderate
The computational predictor REVEL gives a score of 0.904, which is between the ClinGen X-linked IRD VCEP threshold of 0.773 to 0.931 and predicts a damaging effect on RPGR function (PP3_moderate). The computational splicing predictor SpliceAI gives a delta score of 0.01 for acceptor gain, which is below the ClinGen X-linked IRD VCEP threshold of >0.2 and does not predict that the variant disrupts RPGR splicing.
PP4
At least one proband harboring this variant exhibits a phenotype including early onset (1 pt) of night blindness (0.5 pts), decreased central vision acuity (0.5 pts), visual field constriction (0.5 pts), family history consistent with X-linked inheritance (2 pts), delayed or milder phenotype in females (1 pt), and next-generation sequencing-based genotyping identifying no alternative causes of retinal disease (2 pts), which together are specific for RPGR-related recessive retinopathy (7.5 pts, PP4, PMID: 25324289).
PP1_Moderate
The variant has been reported to segregate with retinal dystrophy through at least 3 affected meioses from 1 family. (PP1; PMID: [26316687, 25324289]).
Not Met criteria codes
PS3
Gerasimavicius et al. tried to predict variant effects by protein structural information and molecular mechanisms. This variant was tested as well (PMID: 32958805).

PS4
This variant has been reported in at least 1 proband meeting the PS4 requirement of some functional vision impairment in affected males by age 30, with decreased or absent cone and/or rod ERG responses (PMIDs: 25324289, 26316687, 26427425). Since all three papers have reported the same family, PS4_Supporting was not met.
Curation History
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