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.3407G>A (p.Gly1136Asp)

CA10385145

445488 (ClinVar)

Gene: RPGR
Condition: RPGR-related retinopathy
Inheritance Mode: X-linked inheritance (dominant (HP:0001423))
UUID: 039b677c-7796-4aa8-9b17-6fc73b9cabbf
Approved on: 2025-05-20
Published on: 2025-05-21

HGVS expressions

NM_001034853.2:c.3407G>A
NM_001034853.2(RPGR):c.3407G>A (p.Gly1136Asp)
NC_000023.11:g.38285592C>T
CM000685.2:g.38285592C>T
NC_000023.10:g.38144845C>T
CM000685.1:g.38144845C>T
NC_000023.9:g.38029789C>T
NG_009553.1:g.46944G>A
ENST00000494707.6:c.953+2273G>A
ENST00000642170.1:n.1826+5367G>A
ENST00000642395.2:c.1905+1502G>A
ENST00000642739.1:c.1572+5367G>A
ENST00000644238.1:c.1386+5367G>A
ENST00000644337.1:c.1719+1502G>A
ENST00000645032.1:c.3407G>A
ENST00000645124.1:c.*101+1502G>A
ENST00000646020.1:c.*594+1502G>A
ENST00000318842.11:c.1905+1502G>A
ENST00000339363.7:c.2520+1502G>A
ENST00000378505.6:c.3407G>A
ENST00000465127.1:c.172-380529C>T
ENST00000474584.5:c.*37+5367G>A
ENST00000482855.5:c.1905+1502G>A
ENST00000494707.5:c.139+5367G>A
NM_000328.2:c.1905+1502G>A
NM_001034853.1:c.3407G>A
NM_001367245.1:c.1902+1502G>A
NM_001367246.1:c.1719+1502G>A
NM_001367247.1:c.1572+5367G>A
NM_001367248.1:c.1602+5367G>A
NM_001367249.1:c.1569+5367G>A
NM_001367250.1:c.1569+5367G>A
NM_001367251.1:c.1386+5367G>A
NR_159803.1:n.2263+1502G>A
NR_159804.1:n.1648+5367G>A
NR_159805.1:n.1714+5367G>A
NR_159806.1:n.1866+1502G>A
NR_159807.1:n.1622+5367G>A
NR_159808.1:n.1826+5367G>A
NM_000328.3:c.1905+1502G>A
More

Benign

Met criteria codes 2
BA1 BP4
Not Met criteria codes 1
PS4

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.3407G>A (p.Gly1136Asp) variant is a missense variant encoding the substitution of glycine with aspartic acid at amino acid 1136. The computational predictor REVEL gives a score of 0.053, which is below the ClinGen X-linked IRD VCEP threshold of <0.183 and predicts a non-damaging effect on RPGR function. Additionally, the splicing impact predictor SpliceAI gives a delta score of 0.00, which is below the ClinGen X-linked IRD VCEP recommended threshold of <0.1 and does not strongly predict an impact on splicing (BP4_moderate). This variant is present in gnomAD v.4.1.0 at a frequency of 0.0008861 among hemizygous individuals, with 352 variant alleles / 397,264 total alleles, which is higher than the ClinGen X-linked IRD VCEP BA1 threshold of >0.00005 (BA1). This variant has been reported in at least 1 male proband and 2 females. The male proband had insufficient reported details and did not meet the PS4 requirement of some functional vision impairment in an affected male by age 30 years, or decreased/absent cone and/or rod electroretinogram responses (PMID: 32679846), so PS4_supporting was not met. In summary, this variant is classified as benign 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; BA1 and BP4_moderate. (date of approval 05/16/2025).
Met criteria codes
BA1
This variant is present in gnomAD v.4.0.0 at a frequency of 0.0008861 among hemizygous individuals, with 352 variant alleles / 397264 total alleles, which is higher than the ClinGen X-linked IRD VCEP BA1 threshold of >0.00005 (BA1).
BP4
The computational predictor REVEL gives a score of 0.053, which is below the ClinGen X-linked IRD VCEP threshold of < 0.183 and predicts a non-damaging effect on RPGR function. Additionally, the splicing impact predictor SpliceAI gives a delta score of 0.00, which is below the ClinGen X-linked IRD VCEP recommended threshold of <0.1 and does not strongly predict an impact on splicing (BP4_moderate).
Not Met criteria codes
PS4
This variant has been reported in at least 1 male proband and 2 females. The male proband published data was insufficient and did not meet the PS4 requirement of some functional vision impairment in affected males by age 30, or decreased/absent cone and/or rod ERG responses (PMID: 32679846, PS4_not met).
Curation History
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