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.1059+6G>A

CA10385560

255828 (ClinVar)

Gene: RPGR (HGNC:6103)

Condition: RPGR-related retinopathy (MONDO:0100437)

Inheritance Mode: X-linked inheritance

UUID: 419e2509-9f07-4f06-8a67-8c919cbe6dd4

Approved on: 2025-08-01

Published on: 2025-08-01

HGVS expressions

NM_001034853.2:c.1059+6G>A

NM_001034853.2(RPGR):c.1059+6G>A

NC_000023.11:g.38301241C>T

CM000685.2:g.38301241C>T

NC_000023.10:g.38160494C>T

CM000685.1:g.38160494C>T

NC_000023.9:g.38045438C>T

NG_009553.1:g.31295G>A

ENST00000494707.6:c.263+6G>A

ENST00000642170.1:n.1313+6G>A

ENST00000642395.2:c.1059+6G>A

ENST00000642558.1:c.966+6G>A

ENST00000642739.1:c.1059+6G>A

ENST00000644238.1:c.1059+6G>A

ENST00000644337.1:c.1059+6G>A

ENST00000645032.1:c.1059+6G>A

ENST00000645124.1:c.1059+6G>A

ENST00000646020.1:c.1119+6G>A

ENST00000318842.11:c.1059+6G>A

ENST00000339363.7:c.1059+6G>A

ENST00000378505.6:c.1059+6G>A

ENST00000464437.1:c.125+6G>A

ENST00000465127.1:c.172-364880C>T

ENST00000474584.5:c.1059+6G>A

ENST00000482855.5:c.1059+6G>A

ENST00000494841.1:n.322+6G>A

NM_000328.2:c.1059+6G>A

NM_001034853.1:c.1059+6G>A

NM_001367245.1:c.1056+6G>A

NM_001367246.1:c.1059+6G>A

NM_001367247.1:c.1059+6G>A

NM_001367248.1:c.1089+6G>A

NM_001367249.1:c.1056+6G>A

NM_001367250.1:c.1056+6G>A

NM_001367251.1:c.1059+6G>A

NR_159803.1:n.1261+6G>A

NR_159804.1:n.1110+6G>A

NR_159805.1:n.1201+6G>A

NR_159806.1:n.1201+6G>A

NR_159807.1:n.1201+6G>A

NR_159808.1:n.1313+6G>A

NM_000328.3:c.1059+6G>A

Benign

BA1 BP4

PM2 PM1 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.1059+6G>A an intron 9 variant located six nucleotides after exon 9. This variant is present in gnomAD v4.1.0 at a frequency of 0.0002996 among hemizygous individuals, with 114 variant alleles / 380,467 total alleles, which is higher than the ClinGen X-linked IRD VCEP BA1 threshold of >0.00005 (BA1). The splicing impact predictor SpliceAI gives a delta score of 0.01, which is below the ClinGen X-linked IRD VCEP recommended threshold of <0.1 and does not strongly predict an impact on splicing (BP4). 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 BP4. (date of approval 05/16/2025).

BA1

This variant is present in gnomAD v.4.1.0 at a frequency of 0.0002996 among hemizygous individuals, with 114 variant alleles / 380,467 total alleles, which is higher than the ClinGen X-linked IRD VCEP BA1 threshold of >0.00005 (BA1).

BP4

The splicing impact predictor SpliceAI gives a delta score of 0.01, which is below the ClinGen X-linked IRD VCEP recommended threshold of <0.1 and does not strongly predict an impact on splicing (BP4).

PM2

This variant is present in gnomAD v.2.1.1 at a frequency of [0.0002996] among hemizygous individuals, with [114] variant alleles / [380467] total alleles, which is higher than the ClinGen X-linked IRD VCEP PM2_Supporting threshold of <0.0000005 and fails to meet this criterion.

PM1

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

Curation History

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