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.823G>A (p.Gly275Ser)

CA226447

9899 (ClinVar)

Gene: RPGR
Condition: RPGR-related retinopathy
Inheritance Mode: X-linked inheritance
UUID: ac09a774-f733-4274-8dde-83b5b0a7e9e5
Approved on: 2025-05-20
Published on: 2025-05-20

HGVS expressions

NM_001034853.2:c.823G>A
NM_001034853.2(RPGR):c.823G>A (p.Gly275Ser)
NC_000023.11:g.38304746C>T
CM000685.2:g.38304746C>T
NC_000023.10:g.38163999C>T
CM000685.1:g.38163999C>T
NC_000023.9:g.38048943C>T
NG_009553.1:g.27790G>A
ENST00000494707.6:c.27G>A
ENST00000642170.1:n.1189-3375G>A
ENST00000642373.1:c.*402G>A
ENST00000642395.2:c.823G>A
ENST00000642558.1:c.730G>A
ENST00000642739.1:c.823G>A
ENST00000644238.1:c.823G>A
ENST00000644337.1:c.823G>A
ENST00000645032.1:c.823G>A
ENST00000645124.1:c.823G>A
ENST00000646020.1:c.823G>A
ENST00000647261.1:c.823G>A
ENST00000318842.11:c.823G>A
ENST00000339363.7:c.823G>A
ENST00000378505.6:c.823G>A
ENST00000465127.1:c.172-361375C>T
ENST00000474584.5:c.823G>A
ENST00000482855.5:c.823G>A
ENST00000494841.1:n.86G>A
NM_000328.2:c.823G>A
NM_001034853.1:c.823G>A
NM_001367245.1:c.820G>A
NM_001367246.1:c.823G>A
NM_001367247.1:c.823G>A
NM_001367248.1:c.853G>A
NM_001367249.1:c.820G>A
NM_001367250.1:c.820G>A
NM_001367251.1:c.823G>A
NR_159803.1:n.965G>A
NR_159804.1:n.874G>A
NR_159805.1:n.965G>A
NR_159806.1:n.965G>A
NR_159807.1:n.965G>A
NR_159808.1:n.1189-3375G>A
NM_000328.3:c.823G>A
More

Pathogenic

Met criteria codes 6
PS4_Supporting PP3_Strong PP1_Moderate PM2_Supporting PP4 PS3_Supporting
Not Met criteria codes 1
PM5

Evidence Links 0

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.823G>A (p.Gly275Ser) is a missense variant predicted to cause substitution of glycine by serine at amino acid 275. This variant is absent from hemizygous individuals in gnomAD v4.1.0 (PM2_Supporting). This variant has been reported in at least 4 families, with 1 proband exhibiting a family history consistent with X-linked inheritance, functional vision impairment by age 30 years, decreased cone and rod electroretinogram responses, optic disc pallor, attenuation of vessels, pigmentary retinopathy, abnormal autofluorescence, reduced visual acuity, and abnormal color vision, which together are specific for RPGR-related retinopathy (4 points, PMID: 17480003, PP4). This finding has been combined with reports of the variant in at least 2 additional apparently unrelated probands meeting the requirement of some functional vision impairment in affected males by age 30, with decreased or absent cone and/or rod electroretinogram responses (PMID: 17480003, PMID: 16969763, PS4_Supporting). The variant has been reported to segregate with the phenotype through 12 affected meioses in 2 families, meeting the ClinGen X-linked IRD VCEP PP1_Strong requirement of ≥4 meioses in >1 family (PP1_Strong; PMID: 17480003). At least 4 other missense variants at the same codon (p.Gly275Arg, p.Gly275Cys, p.Gly275Val, and p.Gly275Asp) have been reported in association with retinal disease, however, all of them have a higher Grantham score than this variant, so PM5 is not met. The computational predictor REVEL gives a score of 0.968, which is above the ClinGen X-linked IRD VCEP threshold of >0.932 and predicts a damaging effect on RPGR function (PP3_strong). Fluorescence microscopy-based localization assay performed with the p.Gly275Ser mutant and wild-type RPGR exogenously expressed as GFP-fusion proteins by RPE1 cells showed complete loss of localization to the primary cilia (PMID: 30622176). Tag-based RPGR pull-down from HEK293T cells using anti-Flag beads followed by western blotting-based detection of endogenous PDE6D, RPGRIP1L, or INPP5 showed that the mutant had complete loss of interaction with INPP5E and RPGRIP1L, further indicating a damaging effect on protein function (PMID: 30622176; PS3_Supporting). In summary, this variant meets the criteria to be classified as 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; PS3_Supporting, PS4_Supporting, PM2_Supporting, PP1_Strong, PP3_Strong, and PP4. (date of approval 05/16/2025).
Met criteria codes
PS4_Supporting
This variant has been reported in 2 apparently unrelated families 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 (PMID: 17480003, PMID: 16969763, PS4_supporting).
PP3_Strong
The computational predictor REVEL gives a score of 0.968, which is above the ClinGen X-linked IRD VCEP threshold of >0.932 and predicts a damaging effect on RPGR function (PP3_strong). The computational splicing predictor SpliceAI gives a delta score of 0.08 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.
PP1_Moderate
The variant has been reported to segregate with the phenotype through 12 affected meioses in 2 families, meeting the ClinGen X-linked IRD VCEP PP1_Strong requirement of ≥4 meioses in >1 family (PP1_Strong; PMID: 17480003). A third family was reported, but the available information did not meet the eligibility requirement that affected males should have some functional vision impairment by age 30, with decreased or absent cone and/or rod ERG responses (PMID: 17480003).
PM2_Supporting
This variant is absent from hemizygous individuals in gnomAD v4.1.0 (PM2_Supporting).
PP4
At least 1 patient with this variant displayed a pattern of affected members consistent with X-linked mode of inheritance (2 pts), functional vision impairment by age 30 (required), decreased cone and/or rod ERG responses (required), optic disc pallor (0.5 pts), attenuation of vessels, pigmentary retinopathy (0.5 pts), abnormal hyperfluorescence, visual acuity of 6/15–6/18 (0.5 pts), and abnormal color vision (0.5 pts), which together are specific for RPGR-related retinopathy (4 points, PMID: 17480003, PP4)
PS3_Supporting
Fluorescence microscopy-based localization assay performed with the p.Gly275Ser mutant and wild-type RPGR exogenously expressed as GFP-fusion proteins by RPE1 cells showed complete loss of localization to the primary cilia, indicating that this variant has a damaging effect on protein function (PMID: 30622176). Tag-based RPGR pull-down from HEK293T cells using anti-Flag beads was also performed, with western blotting-based detection of endogenous PDE6D, RPGRIP1L, or INPP5. The mutant showed complete loss of interaction with INPP5E and RPGRIP1L, but not with PDE6D, further indicating a damaging effect on protein function (PMID: 30622176; PS3_supporting).
Not Met criteria codes
PM5
At least 4 other missense variants at the same codon (p.Gly275Arg, p.Gly275Cys, p.Gly275Val, and p.Gly275Asp) have been reported in association with retinal disease, however, all of them have a higher Grantham score than this variant, so PM5 is not met.
Curation History
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