The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_001034853.2:c.934G>C

CA412741115

Gene: RPGR (HGNC:6103)
Condition: RPGR-related retinopathy (MONDO:0100437)
Inheritance Mode: X-linked inheritance
UUID: 5658615a-e1f2-472a-9487-026ccd987913
Approved on: 2026-09-26
Published on: 2026-09-26

HGVS expressions

NM_001034853.2:c.934G>C
NC_000023.11:g.38304635C>G
CM000685.2:g.38304635C>G
NC_000023.10:g.38163888C>G
CM000685.1:g.38163888C>G
NC_000023.9:g.38048832C>G
NG_009553.1:g.27901G>C
ENST00000494707.6:c.138G>C
ENST00000642170.1:n.1189-3264G>C
ENST00000642395.2:c.934G>C
ENST00000642558.1:c.841G>C
ENST00000642739.1:c.934G>C
ENST00000644238.1:c.934G>C
ENST00000644337.1:c.934G>C
ENST00000645032.1:c.934G>C
ENST00000645124.1:c.934G>C
ENST00000646020.1:c.934G>C
ENST00000647261.1:c.934G>C
ENST00000318842.11:c.934G>C
ENST00000339363.7:c.934G>C
ENST00000378505.6:c.934G>C
ENST00000465127.1:c.172-361486C>G
ENST00000474584.5:c.934G>C
ENST00000482855.5:c.934G>C
ENST00000494841.1:n.197G>C
NM_000328.2:c.934G>C
NM_001034853.1:c.934G>C
NM_001367245.1:c.931G>C
NM_001367246.1:c.934G>C
NM_001367247.1:c.934G>C
NM_001367248.1:c.964G>C
NM_001367249.1:c.931G>C
NM_001367250.1:c.931G>C
NM_001367251.1:c.934G>C
NR_159803.1:n.1076G>C
NR_159804.1:n.985G>C
NR_159805.1:n.1076G>C
NR_159806.1:n.1076G>C
NR_159807.1:n.1076G>C
NR_159808.1:n.1189-3264G>C
NM_000328.3:c.934G>C
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Likely Pathogenic

Met criteria codes 5
PP1 PP4 PP3 PS1_Moderate PM2_Supporting

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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
X-linked Inherited Retinal Disease VCEP
The NM_001034853.2(RPGR):c.934G>C variant is a predicted missense variant encoding the substitution of aspartic acid with histidine at amino acid 312. However, the splicing impact predictor SpliceAI gives a score of 0.97 (donor loss), which is above the ClinGen X-linked IRD VCEP recommended threshold of ≥0.2 and predicts a damaging impact on splicing (PP3). The variant is located outside the +/- 1,2 dinucleotide and another variant with the same predicted splicing impact, c.934+1G>T, was previously classified as a pathogenic variant in the same donor/acceptor motif for the RPGR-related X-linked IRD VCEP (PS1_moderate). This variant is absent from hemizygous individuals in gnomAD v4.1.0 (PM2_Supporting). At least one proband harboring this variant exhibits a phenotype including childhood-onset (1), decreased central vision acuity (0.5), night blindness (0.5), optic nerve pallor (0.5), pigmentary retinopathy (0.5), rod cone dystrophy (1), X-linked inheritance (2), which together are specific for RPGR-related recessive retinopathy (6 points, PMID: 36882936, PP4). The variant has been reported to segregate with retinal dystrophy through at least 2 affected meiosis from 1 family. (PP1; PMID: 36882936).In summary, this variant is 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: PS1_moderate, PP3, PP4, PP1, and PM2_supporting.
Met criteria codes
PP1
The variant has been reported to segregate with retinal dystrophy through at least 2 affected meiosis from 1 family. (PP1; PMID: 36882936).
PP4
At least one proband harboring this variant exhibits a phenotype including childhood-onset (1), decreased central vision acuity (0.5), night blindness (0.5), optic nerve pallor (0.5), pigmentary retinopathy (0.5), rod cone dystrophy (1), X-linked inheritance (2), which together are specific for RPGR-related recessive retinopathy (6 points, PMID: 36882936, PP4).
PP3
The splicing impact predictor SpliceAI gives a score of 0.97 (donor loss), which is above the ClinGen X-linked IRD VCEP recommended threshold of ≥0.2 and predicts a damaging impact on splicing (PP3).
PS1_Moderate
This variant is outside the +/- 1,2 dinucleotide and meets the PP3 code due to predicted splicing disruption and another predicted splicing variant, c.934+1G>T, was previously classified as a pathogenic variant in the same donor/acceptor motif for the RPGR-related X-linked IRD VCEP (PS1_moderate).
PM2_Supporting
This variant is absent from hemizygous individuals in gnomAD v4.1.0 (PM2_Supporting).
Curation History
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