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.2667_2669del (p.Glu890del)

Curation Version - 1.0
Curation History
JSON LD for Version 1.0

CA10385255

257196 (ClinVar)

Gene: RPGR

Condition: RPGR-related retinopathy

Inheritance Mode: X-linked inheritance

Link to MONDO

UUID: 4290661a-bccc-495c-aec0-e2580f717499

Approved on: 2025-05-20

Published on: 2025-05-21

HGVS expressions

NM_001034853.2:c.2667_2669del

NM_001034853.2(RPGR):c.2667_2669del (p.Glu890del)

NC_000023.11:g.38286332_38286334del

CM000685.2:g.38286332_38286334del

NC_000023.10:g.38145585_38145587del

CM000685.1:g.38145585_38145587del

NC_000023.9:g.38030529_38030531del

NG_009553.1:g.46204_46206del

ENST00000494707.6:c.953+1533_953+1535del

ENST00000642170.1:n.1826+4627_1826+4629del

ENST00000642395.2:c.1905+762_1905+764del

ENST00000642739.1:c.1572+4627_1572+4629del

ENST00000644238.1:c.1386+4627_1386+4629del

ENST00000644337.1:c.1719+762_1719+764del

ENST00000645032.1:c.2667_2669del

ENST00000645124.1:c.*101+762_*101+764del

ENST00000646020.1:c.*594+762_*594+764del

ENST00000318842.11:c.1905+762_1905+764del

ENST00000339363.7:c.2520+762_2520+764del

ENST00000378505.6:c.2667_2669del

ENST00000465127.1:c.172-379789_172-379787del

ENST00000474584.5:c.*37+4627_*37+4629del

ENST00000482855.5:c.1905+762_1905+764del

ENST00000494707.5:c.139+4627_139+4629del

NM_000328.2:c.1905+762_1905+764del

NM_001034853.1:c.2667_2669del

NM_001367245.1:c.1902+762_1902+764del

NM_001367246.1:c.1719+762_1719+764del

NM_001367247.1:c.1572+4627_1572+4629del

NM_001367248.1:c.1602+4627_1602+4629del

NM_001367249.1:c.1569+4627_1569+4629del

NM_001367250.1:c.1569+4627_1569+4629del

NM_001367251.1:c.1386+4627_1386+4629del

NR_159803.1:n.2263+762_2263+764del

NR_159804.1:n.1648+4627_1648+4629del

NR_159805.1:n.1714+4627_1714+4629del

NR_159806.1:n.1866+762_1866+764del

NR_159807.1:n.1622+4627_1622+4629del

NR_159808.1:n.1826+4627_1826+4629del

NM_000328.3:c.1905+762_1905+764del

Benign

BP3 BA1

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.2667_2669del (p.Glu890del) is a short in-frame deletion of 3 base pairs that encode amino acid 890 within a low-complexity region (PMID: 27162334) that extends approximately from amino acids 787–1043 in RPGR (BP3). This variant is present in gnomAD v.4.1.0 at a frequency of 0.1323 among hemizygous individuals, with 6,699 variant alleles / 50,616 total alleles, which is higher than the ClinGen X-linked IRD VCEP BA1 threshold of >0.00005 (BA1). 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 BP3. (date of approval 05/16/2025).

BP3

This variant is a short in-frame deletion of 3 base pairs that encode amino acids 890 within a low-complexity region (PMID: 27162334) that extends approximately from amino acids 787–1043 in RPGR (BP3).

BA1

This variant is present in gnomAD v.4.1.0 at a frequency of 0.1323 among hemizygous individuals, with 6699 variant alleles / 50616 total alleles, which is higher than the ClinGen X-linked IRD VCEP BA1 threshold of >0.00005 (BA1).

Curation History

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