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.179G>T (p.Gly60Val)

CA226376

9902 (ClinVar)

Gene: RPGR
Condition: RPGR-related retinopathy
Inheritance Mode: X-linked inheritance (dominant (HP:0001423))
UUID: bdcbb5e9-e036-4b2c-b52f-141135ed6a6e
Approved on: 2025-05-21
Published on: 2025-05-21

HGVS expressions

NM_001034853.2:c.179G>T
NM_001034853.2(RPGR):c.179G>T (p.Gly60Val)
NC_000023.11:g.38322921C>A
CM000685.2:g.38322921C>A
NC_000023.10:g.38182174C>A
CM000685.1:g.38182174C>A
NC_000023.9:g.38067118C>A
NG_009553.1:g.9615G>T
ENST00000642170.1:n.589G>T
ENST00000642373.1:c.179G>T
ENST00000642395.2:c.179G>T
ENST00000642558.1:c.154+478G>T
ENST00000642739.1:c.179G>T
ENST00000644238.1:c.179G>T
ENST00000644337.1:c.179G>T
ENST00000645032.1:c.179G>T
ENST00000645124.1:c.179G>T
ENST00000646020.1:c.179G>T
ENST00000647261.1:c.179G>T
ENST00000318842.11:c.179G>T
ENST00000339363.7:c.179G>T
ENST00000378505.6:c.179G>T
ENST00000465127.1:c.172-343200C>A
ENST00000474584.5:c.179G>T
ENST00000482855.5:c.179G>T
NM_000328.2:c.179G>T
NM_001034853.1:c.179G>T
NM_001367245.1:c.179G>T
NM_001367246.1:c.179G>T
NM_001367247.1:c.179G>T
NM_001367248.1:c.209G>T
NM_001367249.1:c.179G>T
NM_001367250.1:c.179G>T
NM_001367251.1:c.179G>T
NR_159803.1:n.321G>T
NR_159804.1:n.321G>T
NR_159805.1:n.321G>T
NR_159806.1:n.321G>T
NR_159807.1:n.321G>T
NR_159808.1:n.589G>T
NM_000328.3:c.179G>T
More

Likely Pathogenic

Met criteria codes 5
PS3_Supporting PP4 PP3_Strong PM2_Supporting PP1_Moderate
Not Met criteria codes 21
PP2 PM1 PM3 PM4 PM5 PM6 BA1 BS2 BS4 BS3 BS1 PS2 PS4 PS1 BP2 BP3 BP4 BP1 PVS1 BP5 BP7

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.179G>T (p.Gly60Val) is a missense variant that replaces glycine with valine at amino acid 60. 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 family history consistent with X-linked inheritance (2 pts) with delayed or milder phenotype in females (1 pt), visual field reduction (0.5 pts), central vision problem (0.5 pts) since 6 years of age (1 pt), poor night vision (0.5 pts), pigmentary retinopathy (0.5 pts), and nondetectable electroretinogram responses, which together are specific for RPGR-related retinopathy (6 points, PMID: 9855162, PP4). This variant has been reported in other publications, however, the ability to conclude that the probands described are unrelated was not successful (PMIDs: 28559085, 10937588, 34985506, 9399904, 9855162). The variant has been reported to segregate with retinal dystrophy through at least 4 meioses from at least 1 family (PP1_moderate; PMID: [9855162]). The computational predictor REVEL gives a score of 0.98, 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 0.19 for acceptor loss, which is below the ClinGen X-linked IRD VCEP threshold of >0.2 and does not predict that the variant disrupts RPGR splicing. Exogenously expressed RPGR harboring the variant exhibits reduced interaction with RPGRIP1 in a yeast-2-hybrid experiment (PMID: 23213406, 23213406, PS3_supporting). 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; PM2_supporting, PP1_moderate, PP3_strong, PS3_supporting, and PP4. (date of approval 05/16/2025).
Met criteria codes
PS3_Supporting
Exogenously expressed RPGR harboring the variant exhibits reduced interaction with RPGRIP1 in a yeast-2-hybrid experiment (PMID: 23213406, 23213406, PS3_Supporting)

PP4
At least one proband harboring this variant exhibits a phenotype including family history consistent with X-linked inheritance (2 pts) with delayed or milder phenotype in females (1 pt), visual field reduction (0.5 pts), central vision problem (0.5 pts) since 6 years of age (1 pt), poor night vision (0.5 pts), pigmentary retinopathy (0.5 pts), and nondetectable electroretinogram responses, which together are specific for RPGR-related retinopathy (6 points, PMID: 9855162, PP4).
PP3_Strong
The computational predictor REVEL gives a score of 0.98, 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 0.19 for acceptor loss, which is below the ClinGen X-linked IRD VCEP threshold of >0.2 and does not predict that the variant disrupts RPGR splicing.
PM2_Supporting
This variant is absent from hemizygous individuals in gnomAD v4.1.0 (PM2_Supporting).
PP1_Moderate
The variant has been reported to segregate with retinal dystrophy through at least 3 affected meioses from at least 1 family. (PP1_Moderate; PMID: [9855162]).
Not Met criteria codes
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
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
BA1
This variant is absent in gnomAD v.2.1.1.
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
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
This variant is absent in gnomAD v.2.1.1.
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
This variant has been reported in other publications, however, the ability to conclude that the probands described are unrelated was not successful (PMIDs: 28559085, 10937588, 34985506, 9399904, 9855162).
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
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
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.