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_001034853.2(RPGR):c.2650G>T (p.Glu884Ter)

CA254931

9908 (ClinVar)

Gene: RPGR (HGNC:6103)
Condition: RPGR-related retinopathy (MONDO:0100437)
Inheritance Mode: X-linked inheritance
UUID: fbca8cdb-cf7e-443f-a261-96f37add5939
Approved on: 2025-09-05
Published on: 2025-09-05

HGVS expressions

NM_001034853.2(RPGR):c.2650G>T (p.Glu884Ter)
NM_001034853.2:c.2650G>T
NC_000023.11:g.38286349C>A
CM000685.2:g.38286349C>A
NC_000023.10:g.38145602C>A
CM000685.1:g.38145602C>A
NC_000023.9:g.38030546C>A
NG_009553.1:g.46187G>T
ENST00000494707.6:c.953+1516G>T
ENST00000642170.1:n.1826+4610G>T
ENST00000642395.2:c.1905+745G>T
ENST00000642739.1:c.1572+4610G>T
ENST00000644238.1:c.1386+4610G>T
ENST00000644337.1:c.1719+745G>T
ENST00000645032.1:c.2650G>T
ENST00000645124.1:c.*101+745G>T
ENST00000646020.1:c.*594+745G>T
ENST00000318842.11:c.1905+745G>T
ENST00000339363.7:c.2520+745G>T
ENST00000378505.6:c.2650G>T
ENST00000465127.1:c.172-379772C>A
ENST00000474584.5:c.*37+4610G>T
ENST00000482855.5:c.1905+745G>T
ENST00000494707.5:c.139+4610G>T
NM_000328.2:c.1905+745G>T
NM_001034853.1:c.2650G>T
NM_001367245.1:c.1902+745G>T
NM_001367246.1:c.1719+745G>T
NM_001367247.1:c.1572+4610G>T
NM_001367248.1:c.1602+4610G>T
NM_001367249.1:c.1569+4610G>T
NM_001367250.1:c.1569+4610G>T
NM_001367251.1:c.1386+4610G>T
NR_159803.1:n.2263+745G>T
NR_159804.1:n.1648+4610G>T
NR_159805.1:n.1714+4610G>T
NR_159806.1:n.1866+745G>T
NR_159807.1:n.1622+4610G>T
NR_159808.1:n.1826+4610G>T
NM_000328.3:c.1905+745G>T
More

Pathogenic

Met criteria codes 4
PS4_Supporting PM2_Supporting PVS1 PP4
Not Met criteria codes 15
BS2 BS4 BS1 BP4 BP3 BP7 PS3 PS1 PS2 BA1 PP3 PP1 PM6 PM5 PM4

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.2650G>T (p.Glu884Ter) is a nonsense variant that introduces a premature stop codon within exon 15 of 15 that is predicted to disrupt a critical C-terminal region required for proper glutamylation of RPGR (PVS1, PMID: 36445968). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). This variant has been reported in at least 2 apparently unrelated probands meeting one of the PS4 requirements of a male with some functional vision impairment by age 30 years and/or decreased or absent electroretinogram responses, or a female with functional visual abnormality and documentation of a male relative affected with retinitis pigmentosa (PMID: 17325176, PMID: 30567410, PS4_Supporting). At least one proband harboring this variant exhibits a phenotype including onset of visual defects before the age of 30 years, fundus autofluorescence imaging showing radial pattern reflex, a family history consistent with X-linked inheritance with no male-to-male transmission (2 pts) and delayed/milder phenotype in females (1 pt), night blindness (0.5 pts), and pigmentary retinopathy (0.5 pts) which together are specific for RPGR-related retinopathy (4 points, PMID: 30567410, PP4). In summary, this variant is 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; PVS1, PS4_Supporting, PM2_Supporting, and PP4.
Met criteria codes
PS4_Supporting
This variant has been reported in at least 2 apparently unrelated probands meeting one of the PS4 requirements of a male with some functional vision impairment by age 30 and/or decreased or absent ERG responses, or a female with functional visual abnormality and documentation of a male relative affected with retinitis pigmentosa (PMID: 17325176, PMID: 30567410, PS4_Supporting).
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting).
PVS1
This is a nonsense variant that introduces a premature stop codon between amino acids 1-1132 is predicted to disrupt a critical C-terminal region required for proper glutamylation of ORF15 of RPGR (PVS1, PMID: 36445968).
PP4
At least one proband harboring this variant exhibits a phenotype including onset of visual defects before the age of 30 years, fundus autofluorescence imaging showing radial pattern reflex, a family history with no male-to-male transmission (2 pts) and delayed/milder phenotype in females (1 pt), night blindness (0.5 pts), and pigmentary retinopathy (0.5 pts) which together are specific for RPGR-related retinopathy (4 points, PMID: 30567410, PP4).
Not Met criteria codes
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No insertions/deletions
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
Causing premature stop/shorter protein
PS1
Not previously examined by VCEP
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
Not previously examined by VCEP
PM4
stop-loss variant
Curation History
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