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(RPGR):c.1693C>T (p.Gln565Ter)

CA412736970

2907569 (ClinVar)

Gene: RPGR (HGNC:6103)

Condition: RPGR-related retinopathy (MONDO:0100437)

Inheritance Mode: X-linked inheritance

UUID: 8b6340ac-c705-4eb4-b43c-4fee589a452c

Approved on: 2026-01-25

Published on: 2026-01-25

HGVS expressions

NM_001034853.2(RPGR):c.1693C>T (p.Gln565Ter)

NM_001034853.2:c.1693C>T

NC_000023.11:g.38287921G>A

CM000685.2:g.38287921G>A

NC_000023.10:g.38147174G>A

CM000685.1:g.38147174G>A

NC_000023.9:g.38032118G>A

NG_009553.1:g.44615C>T

ENST00000494707.6:c.897C>T

ENST00000642170.1:n.1826+3038C>T

ENST00000642395.2:c.1693C>T

ENST00000642739.1:c.1572+3038C>T

ENST00000644238.1:c.1386+3038C>T

ENST00000644337.1:c.1507C>T

ENST00000645032.1:c.1693C>T

ENST00000645124.1:c.1573-676C>T

ENST00000646020.1:c.*386C>T

ENST00000318842.11:c.1693C>T

ENST00000339363.7:c.1693C>T

ENST00000378505.6:c.1693C>T

ENST00000465127.1:c.172-378200G>A

ENST00000474584.5:c.*37+3038C>T

ENST00000482855.5:c.1693C>T

ENST00000494707.5:c.139+3038C>T

NM_000328.2:c.1693C>T

NM_001034853.1:c.1693C>T

NM_001367245.1:c.1690C>T

NM_001367246.1:c.1507C>T

NM_001367247.1:c.1572+3038C>T

NM_001367248.1:c.1602+3038C>T

NM_001367249.1:c.1569+3038C>T

NM_001367250.1:c.1569+3038C>T

NM_001367251.1:c.1386+3038C>T

NR_159803.1:n.2055C>T

NR_159804.1:n.1648+3038C>T

NR_159805.1:n.1714+3038C>T

NR_159806.1:n.1715-676C>T

NR_159807.1:n.1622+3038C>T

NR_159808.1:n.1826+3038C>T

NM_000328.3:c.1693C>T

Pathogenic

PM2_Supporting PVS1 PP1_Moderate

PP4 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.1693C>T (p.Gln565Ter) is a nonsense variant in codon 565 that introduces a premature stop codon into exon 14 of 15, and is predicted to lead to nonsense-mediated decay in the RPGR gene in which loss-of-function is an established mechanism of disease (PVS1). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). At least one female proband (>40) harboring this variant has been confirmed to have an affected male relative and exhibits a delayed phenotype including night blindness, and moderately decreased cone and rod electroretinogram responses (PMID: 31645972). The variant has been reported to segregate with retinal dystrophy through at least 3 affected meioses from 1 family (PP1_Moderate; PMID: 31645972). 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, PM2_Supporting, and PP1_Moderate.

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 into exon 14 of 15, and is predicted to lead to nonsense-mediated decay in the RPGR gene in which loss-of-function is an established mechanism of disease (PVS1).

PP1_Moderate

The variant has been reported to segregate with retinal dystrophy through at least 3 affected meioses from 1 family (PMID: 31645972, PP1_Moderate).

PP4

At least one female proband (>40) harboring this variant exhibits a phenotype including night blindness, moderately decreased cone and rod responses (ERG), and a delayed phenotype. Since no male proband (<30) was described, the required criteria to use PP4 are not met.

PS4

This variant has been reported in at least 1 family (PMID: 31645972). However, 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 not given for the affected male, so PS4 was not met.

Curation History

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