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.667T>C (p.Cys223Arg)

CA254929

9893 (ClinVar)

Gene: RS1 (HGNC:6247)
Condition: X-linked retinoschisis (MONDO:0010725)
Inheritance Mode: X-linked inheritance (recessive (HP:0001419))
UUID: c5bd1381-d759-4a76-8f06-4488b4c637ca
Approved on: 2025-09-19
Published on: 2025-09-19

HGVS expressions

NM_000330.4:c.667T>C
NM_000330.4(RS1):c.667T>C (p.Cys223Arg)
NC_000023.11:g.18642012A>G
CM000685.2:g.18642012A>G
NC_000023.10:g.18660132A>G
CM000685.1:g.18660132A>G
NC_000023.9:g.18570053A>G
NG_008475.1:g.221408A>G
NG_008659.3:g.40437T>C
ENST00000379984.4:c.667T>C
ENST00000379984.3:c.667T>C
ENST00000379989.6:c.2714-3995A>G
ENST00000379996.7:c.2714-3995A>G
ENST00000476595.1:n.1158T>C
NM_000330.3:c.667T>C
NM_001037343.1:c.2714-3995A>G
NM_003159.2:c.2714-3995A>G
NM_001037343.2:c.2714-3995A>G
NM_003159.3:c.2714-3995A>G
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Pathogenic

Met criteria codes 7
PS2_Moderate PP1 PP4 PP3_Strong PM2_Supporting PS4_Moderate PS3_Supporting
Not Met criteria codes 1
PM1

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.667T>C (p.Cys223Arg) is a missense variant encoding the substitution of cysteine with arginine at amino acid 223. This variant is absent from hemizygous individuals in gnomAD v4.1.0 (PM2_Supporting). This variant has been reported in at least 3 apparently unrelated probands meeting the PS4 requirements of a male diagnosed with X-linked retinoschisis (PMID: 34645606, PMID: 10533068, PMID: 30652005, PS4_Moderate). At least one proband harboring this variant exhibits a phenotype including appearance of schisis and reduced visual acuity before age 13 years, which together are specific for X-linked retinoschisis (PMID: 33460243, PP4). This variant has been identified as a de novo occurrence with confirmed parental relationships in an individual meeting the PS2 requirement of some functional vision impairment in affected males by age 13 (1 point, PS2_Moderate, PMID: 33460243). The variant has been reported to segregate with retinal dystrophy through 1 meiosis in a family with two affected brothers (PP1; PMID: 30652005). The computational predictor REVEL gives a score of 0.974, 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. COS‐7 cells exogenously expressing the variant exhibit loss of RS1 secretion into the medium relative to the wild-type control (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). However, the PP3_Strong code has been met, which is ineligible to be used in combination with the PM1 code at any strength, so the PM1 code was not met. In summary, this variant is classified as 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, PS3_Supporting, PP1, PP4, PS2_Moderate, and PS4_Moderate.
Met criteria codes
PS2_Moderate
This variant has been identified as a de novo occurrence with confirmed parental relationships in an individual meeting the PS2 requirement of some functional vision impairment in affected males by age 13 (1 point, PS2_Moderate, PMID: 33460243).
PP1
The variant has been reported to segregate with retinal dystrophy through 1 meiosis in a family- two affected brothers (PP1; PMID: 30652005).
PP4
At least one proband harboring this variant exhibits a phenotype including appearance of schisis and reduced visual acuity before age 13 years, which together are specific for X-linked retinoschisis (PMID: 33460243, PP4).
PP3_Strong
The computational predictor REVEL gives a score of 0.974, 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).
PS4_Moderate
This variant has been reported in at least 3 apparently unrelated probands meeting the PS4 requirements of a male diagnosed with X-linked retinoschisis (PMID: 34645606, PMID: 10533068, PMID: 30652005, PS4_Moderate)
PS3_Supporting
COS‐7 cells exogenously expressing the variant exhibit loss of RS1 secretion into the medium relative to the wild-type control (PMID: 16361673, PS3_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). However, the PP3_Strong code has been met, which is ineligible to be used in combination with the PM1 code at any strength, so the PM1 code was not met.
Curation History
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