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.141T>G (p.Ser47=)

CA226360

98741 (ClinVar)

Gene: RPGR (HGNC:6103)

Condition: RPGR-related retinopathy (MONDO:0100437)

Inheritance Mode: X-linked inheritance

UUID: addc7984-3ab1-4e7c-9ca2-8980bd438504

Approved on: 2025-10-05

Published on: 2025-10-06

HGVS expressions

NM_001034853.2:c.141T>G

NM_001034853.2(RPGR):c.141T>G (p.Ser47=)

NC_000023.11:g.38323412A>C

CM000685.2:g.38323412A>C

NC_000023.10:g.38182665A>C

CM000685.1:g.38182665A>C

NC_000023.9:g.38067609A>C

NG_009553.1:g.9124T>G

ENST00000642170.1:n.551T>G

ENST00000642373.1:c.141T>G

ENST00000642395.2:c.141T>G

ENST00000642558.1:c.141T>G

ENST00000642739.1:c.141T>G

ENST00000644238.1:c.141T>G

ENST00000644337.1:c.141T>G

ENST00000645032.1:c.141T>G

ENST00000645124.1:c.141T>G

ENST00000646020.1:c.141T>G

ENST00000647261.1:c.141T>G

ENST00000318842.11:c.141T>G

ENST00000339363.7:c.141T>G

ENST00000378505.6:c.141T>G

ENST00000465127.1:c.172-342709A>C

ENST00000474584.5:c.141T>G

ENST00000482855.5:c.141T>G

NM_000328.2:c.141T>G

NM_001034853.1:c.141T>G

NM_001367245.1:c.141T>G

NM_001367246.1:c.141T>G

NM_001367247.1:c.141T>G

NM_001367248.1:c.171T>G

NM_001367249.1:c.141T>G

NM_001367250.1:c.141T>G

NM_001367251.1:c.141T>G

NR_159803.1:n.283T>G

NR_159804.1:n.283T>G

NR_159805.1:n.283T>G

NR_159806.1:n.283T>G

NR_159807.1:n.283T>G

NR_159808.1:n.551T>G

NM_000328.3:c.141T>G

Benign

BA1 BP4 BP7

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.141T>G (p.Ser47=) is a synonymous variant in exon 2 of RPGR (BP7). The splicing impact predictor SpliceAI gives a delta score of 0.00, which is below the ClinGen X-linked IRD VCEP recommended threshold of <0.1 and does not strongly predict an impact on splicing (BP4). This variant is present in gnomAD v.4.1.0 at a frequency of 0.0004126 among hemizygous individuals, with 162 variant alleles / 392,654 total hemizygous 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, BP4, and BP7.

BA1

This variant is present in gnomAD v.4.1.0 at a frequency of 0.0004126 among hemizygous individuals, with 162 variant alleles/392654 total hemizygous 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 0.00, which is below the ClinGen X-linked IRD VCEP recommended threshold of <0.1 and does not strongly predict an impact on splicing (BP4).

BP7

This silent variant NM_001034853.2(RPGR):c.141T>G causing a synonymous variant at codon 42 does not have an impact at splicing sites according to SpliceAI, which predicts a delta score of 0.00 for all splicing types, which is below the ClinGen X-linked IRD VCEP recommended threshold of <0.1 and does not strongly predict an impact on splicing (BP7).

Curation History

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