The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000330.4(RS1):c.655T>G (p.Cys219Gly)

CA226843

99016 (ClinVar)

Gene: RS1 (HGNC:6247)
Condition: X-linked retinoschisis (MONDO:0010725)
Inheritance Mode: X-linked inheritance (recessive (HP:0001419))
UUID: b2159f7e-5a9a-446f-8c66-b4a3a7712b54
Approved on: 2025-10-04
Published on: 2025-10-05

HGVS expressions

NM_000330.4(RS1):c.655T>G (p.Cys219Gly)
NM_000330.4:c.655T>G
NC_000023.11:g.18642024A>C
CM000685.2:g.18642024A>C
NC_000023.10:g.18660144A>C
CM000685.1:g.18660144A>C
NC_000023.9:g.18570065A>C
NG_008475.1:g.221420A>C
NG_008659.3:g.40425T>G
ENST00000379984.4:c.655T>G
ENST00000379984.3:c.655T>G
ENST00000379989.6:c.2714-3983A>C
ENST00000379996.7:c.2714-3983A>C
ENST00000476595.1:n.1146T>G
NM_000330.3:c.655T>G
NM_001037343.1:c.2714-3983A>C
NM_003159.2:c.2714-3983A>C
NM_001037343.2:c.2714-3983A>C
NM_003159.3:c.2714-3983A>C
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Likely Pathogenic

Met criteria codes 3
PS3_Supporting PP3_Strong PM2_Supporting
Not Met criteria codes 2
PM1 PS4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen X-linked Inherited Retinal Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RS1 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_000330.4(RS1):c.655T>G (p.Cys219Gly) is a missense variant encoding the substitution of cysteine with glycine at amino acid 219. This variant is absent from hemizygous individuals in gnomAD v4.1.0 (PM2_Supporting). This variant has been reported in at least 1 proband meeting the PS4 requirement of a male diagnosed with X-linked retinoschisis (PMID: 9618178, PMID: 15937075). However, PS4_Supporting requires at least 2 unrelated probands, so this criterion was not met. The computational predictor REVEL gives a score of 0.984, which is above the ClinGen X-linked IRD VCEP threshold of >0.932 and predicts a damaging effect on RS1 function (PP3_Strong). The computational splicing predictor SpliceAI gives a delta score of 0.00 for all predictive splice changes, which is below the ClinGen X-linked IRD VCEP threshold of ≥0.2 and does not predict that the variant disrupts RS1 splicing. Exogenously expressed RS1 harboring the variant was subjected to gel filtration-based separation and PAGE analysis on a non‐reducing gel and exhibits defective oligomerization indicating no formation of octamers (PMID: 16361673, PS3_Supporting). This variant is a missense substitution affecting a critical amino acid residue involved in disulfide bridge formation as defined by the ClinGen X-linked IRD VCEP (PMID: 26812435). PM1_Strong is not met as this code is ineligible to be used in combination with PP3_Strong. In summary, this variant is classified as likely pathogenic for X-linked retinoschisis based on the ClinGen X-linked Inherited Retinal Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for RS1 Version 1.0.0: PM2_Supporting, PP3_Strong, and PS3_Supporting.
Met criteria codes
PS3_Supporting
Exogenously expressed RS1 harboring the variant was subjected to gel filtration-based separation and PAGE analysis on a non‐reducing gel and exhibits defective oligomerization indicating no formation of octamers (PMID: 16361673, PS3_Supporting).
PP3_Strong
The computational predictor REVEL gives a score of 0.984, which is above the ClinGen X-linked IRD VCEP threshold of >0.932 and predicts a damaging effect on RS1 function (PP3_Strong). The computational splicing predictor SpliceAI gives a delta score of 0.00 for all predictive splice changes, which is below the ClinGen X-linked IRD VCEP threshold of ≥0.2 and does not predict that the variant disrupts RS1 splicing.
PM2_Supporting
This variant is absent from hemizygous individuals in gnomAD v4.1.0 (PM2_Supporting).
Not Met criteria codes
PM1
This variant is a missense substitution affecting a critical amino acid residue involved in disulfide bridge formation as defined by the ClinGen X-linked IRD VCEP (PMID: 26812435). PM1_Strong is not met as this code is ineligible to be used in combination with PP3_Strong.
PS4
This variant has been reported in at least 1 proband meeting the PS4 requirement of a male diagnosed with X-linked retinoschisis (PMID: 9618178, PMID: 15937075). However, PS4_Supporting requires at least 2 unrelated probands, so this criterion was not met.
Curation History
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