Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Variant: NM_001034853.2:c.1636G>T

CA412737308

Gene: RPGR (HGNC:6103)

Condition: RPGR-related retinopathy (MONDO:0100437)

Inheritance Mode: X-linked inheritance (primarily recessive with milder female expression)

UUID: 8a62de89-5b4c-4c09-8915-de408c7f26fd

Approved on: 2025-09-07

Published on: 2025-09-07

HGVS expressions

NM_001034853.2:c.1636G>T

NC_000023.11:g.38287978C>A

CM000685.2:g.38287978C>A

NC_000023.10:g.38147231C>A

CM000685.1:g.38147231C>A

NC_000023.9:g.38032175C>A

NG_009553.1:g.44558G>T

ENST00000494707.6:c.840G>T

ENST00000642170.1:n.1826+2981G>T

ENST00000642395.2:c.1636G>T

ENST00000642739.1:c.1572+2981G>T

ENST00000644238.1:c.1386+2981G>T

ENST00000644337.1:c.1450G>T

ENST00000645032.1:c.1636G>T

ENST00000645124.1:c.1573-733G>T

ENST00000646020.1:c.*329G>T

ENST00000318842.11:c.1636G>T

ENST00000339363.7:c.1636G>T

ENST00000378505.6:c.1636G>T

ENST00000465127.1:c.172-378143C>A

ENST00000474584.5:c.*37+2981G>T

ENST00000482855.5:c.1636G>T

ENST00000494707.5:c.139+2981G>T

NM_000328.2:c.1636G>T

NM_001034853.1:c.1636G>T

NM_001367245.1:c.1633G>T

NM_001367246.1:c.1450G>T

NM_001367247.1:c.1572+2981G>T

NM_001367248.1:c.1602+2981G>T

NM_001367249.1:c.1569+2981G>T

NM_001367250.1:c.1569+2981G>T

NM_001367251.1:c.1386+2981G>T

NR_159803.1:n.1998G>T

NR_159804.1:n.1648+2981G>T

NR_159805.1:n.1714+2981G>T

NR_159806.1:n.1715-733G>T

NR_159807.1:n.1622+2981G>T

NR_159808.1:n.1826+2981G>T

NM_000328.3:c.1636G>T

Likely Pathogenic

PM2_Supporting PVS1

PS4

Evidence Links 0

Expert Panel

X-linked Inherited Retinal Disease VCEP

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.1636G>T (p.Glu546Ter) is a nonsense variant introducing a premature stop in codon 546 within exon 4 of 15, which is predicted to trigger nonsense-mediated decay (PVS1). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). This variant has been reported in at least 1 proband with a diagnosis of retinitis pigmentosa (PMID: 23372056), however, the number of individuals meeting one of the PS4 requirements of some functional vision impairment in an affected male 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.

PM2_Supporting

This variant is absent from gnomAD v4.0.0 (PM2_Supporting).

PVS1

This is a nonsense 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).

PS4

This variant has been reported in at least 1 proband with a reported diagnosis of retinitis pigmentosa (PMID: 23372056), however, the number of individuals meeting one of the PS4 requirements of some functional vision impairment in an affected male by age 30 years, and/or decreased or absent cone and/or rod electroretinogram responses was fewer than the requirement of at least 2 unrelated probands, so PS4_Supporting was not met.

Curation History

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