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.3034del (p.Glu1012fs)

CA2424844266

1012646 (ClinVar)

Gene: RPGR (HGNC:6103)
Condition: RPGR-related retinopathy (MONDO:0100437)
Inheritance Mode: X-linked inheritance
UUID: a8e50325-a34e-43a6-878c-8627c01f96ea
Approved on: 2025-09-06
Published on: 2025-09-07

HGVS expressions

NM_001034853.2:c.3034del
NM_001034853.2(RPGR):c.3034del (p.Glu1012fs)
NC_000023.11:g.38285965del
CM000685.2:g.38285965del
NC_000023.10:g.38145218del
CM000685.1:g.38145218del
NC_000023.9:g.38030162del
NG_009553.1:g.46571del
ENST00000494707.6:c.953+1900del
ENST00000642170.1:n.1826+4994del
ENST00000642395.2:c.1905+1129del
ENST00000642739.1:c.1572+4994del
ENST00000644238.1:c.1386+4994del
ENST00000644337.1:c.1719+1129del
ENST00000645032.1:c.3034del
ENST00000645124.1:c.*101+1129del
ENST00000646020.1:c.*594+1129del
ENST00000318842.11:c.1905+1129del
ENST00000339363.7:c.2520+1129del
ENST00000378505.6:c.3034del
ENST00000465127.1:c.172-380156del
ENST00000474584.5:c.*37+4994del
ENST00000482855.5:c.1905+1129del
ENST00000494707.5:c.139+4994del
NM_000328.2:c.1905+1129del
NM_001034853.1:c.3034del
NM_001367245.1:c.1902+1129del
NM_001367246.1:c.1719+1129del
NM_001367247.1:c.1572+4994del
NM_001367248.1:c.1602+4994del
NM_001367249.1:c.1569+4994del
NM_001367250.1:c.1569+4994del
NM_001367251.1:c.1386+4994del
NR_159803.1:n.2263+1129del
NR_159804.1:n.1648+4994del
NR_159805.1:n.1714+4994del
NR_159806.1:n.1866+1129del
NR_159807.1:n.1622+4994del
NR_159808.1:n.1826+4994del
NM_000328.3:c.1905+1129del
More

Likely Pathogenic

Met criteria codes 2
PM2_Supporting PVS1
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.3034del (p.Glu1012LysfsTer?) is a frameshift variant due to a 1-nucleotide deletion introducing a premature stop codon in exon 15 of 15, which is predicted to disrupt a critical C-terminal region required for proper glutamylation of RPGR (PVS1, PMID: 36445968). This variant was confirmed to result in a 40% decrease in glutamylation of RPGR when co-transfected into HEK293 cells with the glutamylase TTLL5 (PMID: 36445968), however, PS3_Supporting was not scored as PVS1 has already been met. This variant is absent from gnomAD v4.1.0 (PM2_Supporting). This variant has been reported in at least 2 apparently unrelated probands (PMIDs: 36445968, 30543658). However, the number of individuals meeting the PS4 requirement of some functional vision impairment in affected males by age 30 years, and/or decreased or absent electroretinogram responses was fewer than the requirement of at least 2 unrelated probands, so PS4_Supporting was not met. 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; PVS1 and PM2_Supporting.
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting).
PVS1
This is a frameshift variant that introduces a premature stop codon between amino acids 1-1132 that is predicted to either trigger nonsense-mediated decay or to disrupt a critical C-terminal region required for proper glutamylation of RPGR (PVS1, PMID: 36445968).
Not Met criteria codes
PS3
This variant resulted caused a 40% decrease in glutamylation of RPGR when co-transfected into HEK293 cells with the glutamylase TTLL5 (PMID: 36445968), however, PS3_Supporting was not scored as PVS1 has already been met.

PS4
This variant has been reported in at least 2 apparently unrelated probands (PMIDs: 36445968, 30543658). However, the number of individuals 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 was fewer than the requirement of at least 2 unrelated probands, so PS4_Supporting was not met.
Curation History
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