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.2606_2620del (p.Glu869_Glu873del)

Curation Version - 1.0
Curation History
JSON LD for Version 1.0

CA10385260

237686 (ClinVar)

Gene: RPGR

Condition: RPGR-related retinopathy

Inheritance Mode: X-linked inheritance

Link to MONDO

UUID: 87ac5ad1-14e6-444a-ba8d-67fbfe83867f

Approved on: 2025-05-20

Published on: 2025-05-21

HGVS expressions

NM_001034853.2:c.2606_2620del

NM_001034853.2(RPGR):c.2606_2620del (p.Glu869_Glu873del)

NC_000023.11:g.38286380_38286394del

CM000685.2:g.38286380_38286394del

NC_000023.10:g.38145633_38145647del

CM000685.1:g.38145633_38145647del

NC_000023.9:g.38030577_38030591del

NG_009553.1:g.46143_46157del

ENST00000494707.6:c.953+1472_953+1486del

ENST00000642170.1:n.1826+4566_1826+4580del

ENST00000642395.2:c.1905+701_1905+715del

ENST00000642739.1:c.1572+4566_1572+4580del

ENST00000644238.1:c.1386+4566_1386+4580del

ENST00000644337.1:c.1719+701_1719+715del

ENST00000645032.1:c.2606_2620del

ENST00000645124.1:c.*101+701_*101+715del

ENST00000646020.1:c.*594+701_*594+715del

ENST00000318842.11:c.1905+701_1905+715del

ENST00000339363.7:c.2520+701_2520+715del

ENST00000378505.6:c.2606_2620del

ENST00000465127.1:c.172-379741_172-379727del

ENST00000474584.5:c.*37+4566_*37+4580del

ENST00000482855.5:c.1905+701_1905+715del

ENST00000494707.5:c.139+4566_139+4580del

NM_000328.2:c.1905+701_1905+715del

NM_001034853.1:c.2606_2620del

NM_001367245.1:c.1902+701_1902+715del

NM_001367246.1:c.1719+701_1719+715del

NM_001367247.1:c.1572+4566_1572+4580del

NM_001367248.1:c.1602+4566_1602+4580del

NM_001367249.1:c.1569+4566_1569+4580del

NM_001367250.1:c.1569+4566_1569+4580del

NM_001367251.1:c.1386+4566_1386+4580del

NR_159803.1:n.2263+701_2263+715del

NR_159804.1:n.1648+4566_1648+4580del

NR_159805.1:n.1714+4566_1714+4580del

NR_159806.1:n.1866+701_1866+715del

NR_159807.1:n.1622+4566_1622+4580del

NR_159808.1:n.1826+4566_1826+4580del

NM_000328.3:c.1905+701_1905+715del

Benign

BA1 BP3

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.2606_2620del (p.Glu869_Glu873del) is a short in-frame deletion of 15 nucleotides that encode amino acids 869–873 within a low-complexity region (PMID: 27162334) that extends approximately from amino acids 787–1043 in RPGR (BP3). This variant is present in gnomAD v4.1.0 at a frequency of 0.007397 among hemizygous individuals, with 1,400 variant alleles / 189,256 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).

BA1

This variant is present in gnomAD v4.1.0 at a frequency of 0.007397 among hemizygous individuals, with 1400 variant alleles / 189256 total alleles, which is higher than the ClinGen X-linked IRD VCEP BA1 threshold of >0.00005 (BA1).

BP3

This variant is a short in-frame deletion of 15 base pairs that encode amino acids 869 – 873 within a low-complexity region (PMID: 27162334) that extends approximately from amino acids 787–1043 in RPGR (BP3).

Curation History

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